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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgagtttcttccccctcaattcttagttatgttcagatataatgctcttggtactctcatcctcccatggcttagttgttcaacttcttgatggttgcagACTGATACTAAGAAGATTTCAGCAGTTTCGATATTCTTTGAGACAATGCCCTACAGATTGGATGAAAGCACTGGCTTGATTGATTATGATCAG

Basic information

species Oryza sativa
transcript LOC_Os03g52840.3
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g52840.2 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM2G135283_T01 (Zea mays), 3'ss of exon 6
---------tgagtttc--ttccccctcaattcttagttatgttcagatataatgctcttggtactctcatcctcccatggcttagttgttcaacttcttgatggttgcagACTGATACTAAGAAGATTTCAGCAGTTTCGATATTCTTTGAGACAATGCCCTACAGATTGGATGAAAGCACTGGCTTGATTGATTATGATCAG-------
         ||| |  |  || ||| | |||||||||| |  ||||||||| ||||||| | |||||        | || ||| |   |||| || |  ||    ||||||||||| ||||||||||| || |||  ||| ||||| |||||||||||||| ||||||||||||||||||||||| ||||||||||| ||||||       
atctgcaaatgaatgacattttcccataaattcttagtaacattcagatatgatgctctagatactc--------ctatagctcaaaggttctacctactg---tttgcagACTGACACTAAGAAGATATCTGCAACTTCAATATTTTTTGAGACAATGCCTTACAGATTGGATGAAAGCACTGGATTGATTGATTACGATCAGGTCATTT

upper sequence: LOC_Os03g52840.2 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM2G135283_T02 (Zea mays), 3'ss of exon 6
---------tgagtttc--ttccccctcaattcttagttatgttcagatataatgctcttggtactctcatcctcccatggcttagttgttcaacttcttgatggttgcagACTGATACTAAGAAGATTTCAGCAGTTTCGATATTCTTTGAGACAATGCCCTACAGATTGGATGAAAGCACTGGCTTGATTGATTATGATCAG
         ||| |  |  || ||| | |||||||||| |  ||||||||| ||||||| | |||||        | || ||| |   |||| || |  ||    ||||||||||| ||||||||||| || |||  ||| ||||| |||||||||||||| ||||||||||||||||||||||| ||||||||||| ||||||
atctgcaaatgaatgacattttcccataaattcttagtaacattcagatatgatgctctagatactc--------ctatagctcaaaggttctacctactg---tttgcagACTGACACTAAGAAGATATCTGCAACTTCAATATTTTTTGAGACAATGCCTTACAGATTGGATGAAAGCACTGGATTGATTGATTACGATCAG

upper sequence: LOC_Os03g52840.2 (Oryza sativa), 3'ss of exon 6
lower sequence: GLYMA08G37270.1 (Glycine max), 3'ss of exon 6
tgagtttcttccccctcaattcttagttatgt--tcagatat---aatgctcttggtactctcatcctcc-catggcttagttgttcaacttcttgatggttgcagACTGATACTAAGAAGATTTCAGCAGTTTCGATATTCTTTGAGACAATGCCCTACAGATTGGATGAAAGCACTGGCTTGATTGATTATGATCAG
  |   |||  |   |  ||| | | | ||||    || | |   ||| | ||| | |   ||||  ||  |||    || |  | | ||| ||       ||||||||||||| || ||||| || ||||| |||||||| |||||||||||||| ||  ||||| ||||||| || || |  || || ||||| |||
acaagctctatcagttgtattttaattcatgtaacaagctctctcaattcacttagcatcttcattatctgcatctaatattgctgctactacta------tgcagACTGATACCAAAAAGATATCTGCAGTCTCGATATTTTTTGAGACAATGCCATATCGATTGAATGAAAGTACAGGATACATCGACTATGACCAG

upper sequence: LOC_Os03g52840.2 (Oryza sativa), 3'ss of exon 6
lower sequence: GLYMA14G36280.1 (Glycine max), 3'ss of exon 6
tgagtttcttcccc--ctcaattcttagttatgttcagatataatgctct-tggtactctcatcctcccatggcttagttgttcaacttcttgatggttgcagACTGATACTAAGAAGATTTCAGCAGTTTCGATATTCTTTGAGACAATGCCCTACAGATTGGATGAAAGCACTGGCTTGATTGATTATGATCAG
 |  |||| |   |  |||   |   |  | | || |  | ||    | | ||  |   || |  |  || |  |   ||| | |  |  |||     |||||||||| || |||||||| || || || || ||||||||||| |||||||| ||||||||| |||| |||||||| |  || |||||||| |||
agcctttcattagcaactccccttgcacctcttttaaattgtagcaatgtgtgccatattctttgtaacaagatt---ttgattatttgtttgtatcatgcagACTGACACCAAGAAGATATCGGCTGTATCTATATTCTTTGAAACAATGCCATACAGATTGAATGAGAGCACTGGTTATATCGATTATGACCAG

upper sequence: LOC_Os03g52840.2 (Oryza sativa), 3'ss of exon 6
lower sequence: AT5G26780.3 (Arabidopsis thaliana), 3'ss of exon 6
-----------tgagtttcttccccct---caattcttagtt-atgttcagatataatgctcttg--gtactctcatcct-cccatggcttagttgttcaacttcttgatggttgcagACTGATACTAAGAAGATTTCAGCAGTTTCGATATTCTTTGAGACAATGCCCTACAGATTGGATGAAAGCACTGGCTTGATTGATTATGATCAG
             ||| |||    | |   || |   || || |  |||   | | ||    |||  | | |   ||  |  |  |  || | || ||  | ||  |  ||  |||||||||| || ||||| || || || || || || || |||||||||||||| |||||||||||||| | |||||| |  ||||||||||| |||
gtacttgggttctagtctctctagcttggtcagtcagtatttgactttcttttctcatctctttgtggaattgatattgtatcttttcctcatttcttttatttgctcttg--tgcagACTGACACGAAGAAAATATCGGCTGTATCCATCTTTTTTGAGACAATGCCATACAGATTGGATGAGAACACTGGTTACATTGATTATGACCAG

upper sequence: LOC_Os03g52840.2 (Oryza sativa), 3'ss of exon 6
lower sequence: AT4G37930.1 (Arabidopsis thaliana), 3'ss of exon 6
tgagtttcttccccctcaattcttagttatgttcagatataatgctcttggtactctcatcctcccatggctta-gttgttcaacttcttgatggttg-cagACTGATACTAAGAAGATTTCAGCAGTTTCGATATTCTTTGAGACAATGCCCTACAGATTGGATGAAAGCACTGGCTTGATTGATTATGATCAG
                    |   |||||  ||   || | |   | | || ||||||   |||  |||  | |   | |    ||||||  |  |   |||||||| || |||||||| ||||| || || || |||||||| ||||||||||| |||||||| || ||||||||||  || || || ||||||
---------------gtgccttcaagttaactttgtatgtca---tttcggaactctctgactctgatgaataacagtttctttcttcttatttctcatcagACTGACACCAAGAAGATATCAGCTGTGTCTATCTTCTTTGAAACAATGCCCTATAGATTGGACGAGAGCACTGGCTACATCGACTACGATCAG

upper sequence: LOC_Os03g52840.2 (Oryza sativa), 3'ss of exon 6
lower sequence: Vv00s0211g00160.t01 (Vitis vinifera), 3'ss of exon 6
tgagtttcttccccctcaattcttagttatgttca-gatataatgctcttggtactctcatcctcccatggcttagttgttcaacttcttgatggt-tgcagACTGATACTAAGAAGATTTCAGCAGTTTCGATATTCTTTGAGACAATGCCCTACAGATTGGATGAAAGCACTGGCTTGATTGATTATGATCAG-------
   ||||||      | |     |     ||||   | ||| ||   ||| |   ||| ||   |    |  | |  |  |||  |  | | |  | ||||||| || || ||||| || || ||||| || ||||| |||||||||||||| || |||||| |||| ||||||||||  ||||| ||||| |||       
-aggtttctaatatttgatgatctctccttgtttgtggtattat-tactttgccttcttatgtgctagggagtaacctcctcatttcttcgctattgtgcagACCGACACCAAGAAAATATCTGCAGTGTCTATATTTTTTGAGACAATGCCATATAGATTGAATGAGAGCACTGGCTACATTGACTATGACCAGGTAACTT

upper sequence: LOC_Os03g52840.2 (Oryza sativa), 3'ss of exon 6
lower sequence: Vv00s0211g00120.t01 (Vitis vinifera), 3'ss of exon 6
tgagtttcttccccctcaattcttagttatgttca-gatataatgctcttggtactctcatcctcccatggc--ttagttgttcaacttcttgatggt-tgcagACTGATACTAAGAAGATTTCAGCAGTTTCGATATTCTTTGAGACAATGCCCTACAGATTGGATGAAAGCACTGGCTTGATTGATTATGATCAG
   ||||||      | |     |     ||||   | ||| ||   ||| |   ||| ||   |    | |  | |  |  |||  |  | | |  | ||||||| || || ||||| || || ||||| || ||||| |||||||||||||| || |||||| |||| ||||||||||  ||||| ||||| |||
---gtttctaatatttgatgatctctccttgtttgtggtattat-tactttgccttcttatgtgctagggacagtaacctcctcatttcttcgctattgtgcagACCGACACCAAGAAAATATCTGCAGTGTCTATATTTTTTGAGACAATGCCATATAGATTGAATGAGAGCACTGGCTACATTGACTATGACCAG

upper sequence: LOC_Os03g52840.2 (Oryza sativa), 3'ss of exon 6
lower sequence: Vv00s0211g00100.t01 (Vitis vinifera), 3'ss of exon 6
tgagtttcttccccctcaattcttagttatgttca-gatataatgctcttggtactctcatcctcccatggc--ttagttgttcaacttcttgatggt-tgcagACTGATACTAAGAAGATTTCAGCAGTTTCGATATTCTTTGAGACAATGCCCTACAGATTGGATGAAAGCACTGGCTTGATTGATTATGATCAG
   ||||||      | |     |     ||||   | ||| ||   ||| |   ||| ||   |    | |  | |  |  |||  |  ||| |  | |||||||||| || ||||| || || ||||| || ||||| |||||||||||||| || |||||| |||| ||||||||||  ||||| ||||| |||
---gtttctaatatttgaggatctctccttgtttgtggtattat-tactttgccttcttatgtgctagggacagtaacctcctcatttctttgctattgtgcagACTGACACCAAGAAAATATCTGCAGTGTCTATATTTTTTGAGACAATGCCATATAGATTGAATGAGAGCACTGGCTACATTGACTATGACCAG

upper sequence: LOC_Os03g52840.2 (Oryza sativa), 3'ss of exon 6
lower sequence: Vv18s0001g07960.t01 (Vitis vinifera), 3'ss of exon 6
---tgagtttcttccccctcaattcttagttatgttcagatataatgctcttggtactctcatcctcccatggcttagttgttcaacttcttgatgg----ttgcagACTGATACTAAGAAGATTTCAGCAGTTTCGATATTCTTTGAGACAATGCCCTACAGATTGGATGAAAGCACTGGCTTGATTGATTATGATCAG
   ||||         | ||  | |||  || | ||  |||| || |||     |    |||   ||  |||   ||| | |||| | |  |  |      |||||||| || || |||||||| || || || || ||||| |||||||||||||| ||||||||||||||||  ||||| |  ||||| ||||| |||
atttgaggaataatttcttct-tcctttttttttttttgata-aaagct-----tgtcttcagtatctgatgtgctagcttttcatcattcttttaacattttgcagACCGACACCAAGAAGATATCTGCTGTGTCTATATTTTTTGAGACAATGCCATACAGATTGGATGAAAAAACTGGATATATTGACTATGACCAG

upper sequence: LOC_Os03g52840.2 (Oryza sativa), 3'ss of exon 6
lower sequence: PP1S21_270V6.1 (Physcomitrella patens), 3'ss of exon 6
----------------------------------------------tgagtttcttccccctcaat-tcttagttatgtt--cagatataatgc-tcttggtactctcatcctc--ccatggcttagttg----ttcaacttcttgatggttg-cagACTGATACTAAGAAGATTTCAGCAGTTTCGATATTCTTTGAGACAATGCCCTACAGATTGGATGAAAGCACTGGCTTGATTGATTATGATCAG
                                               |  |||  ||   || ||| || ||     |||  ||    || | | | |  | ||  |  ||| |   ||||  ||  ||     ||||   | || ||||    ||||||||||| |||||||||||||| ||||| || ||||| ||||| |||||||||||| || | ||   ||| || |  || || |||||||||
gtacgtcttctggttttctattcatgcccaatttatacttgcttgtggtatttgctcaaactgaatatcctaagatggttgccattcttactacgtatctgcacgtttctccacaatcatgaatttattcacacttcatgcttttcatggcaaacagACTGATACAAAGAAGATTTCAGCCGTTTCCATTTTCTTCGAGACTATGCCCTACAGACTGAACGAGTCCACAGGTTATATCGACTATGATCAG

Mapped EST sequences

Showing partial alignments of ESTs and genomic sequences. See full alignments


 ATGC     EST sequence
 ATGC     genomic sequence (exon)
 ATGC     genomic sequence (truncated intron)


EST: gi|25798315|gb|CA754276.1|CA754276
EST:     TCATGGCTTTGGATCTTCCTCATGGTGGACATCTTTCTCACGGCTACCAG                         ACTGATACTAAGAAGATTTCAGCAGTTTCGATATTCTTTGAGACAATGCCC
genomic: TCATGGCTTTGGATCTTCCTCATGGTGGACATCTTTCTCACGGCTACCAGgtacatgggt ... atggttgcagACTGATACTAAGAAGATTTCAGCAGTTTCGATATTCTTTGAGACAATGCCC
EST: gi|58689542|gb|CK078229.1|CK078229
EST:     TCATGGCTTTGGATCTTCCTCATGGTGGACATCTTTCTCACGGCTACCAG                         ACTGATACTAAGAAGATTTCAGCAGTTTCGATATTCTTTGAGACAATGCCC
genomic: TCATGGCTTTGGATCTTCCTCATGGTGGACATCTTTCTCACGGCTACCAGgtacatgggt ... atggttgcagACTGATACTAAGAAGATTTCAGCAGTTTCGATATTCTTTGAGACAATGCCC
EST: gi|38472528|gb|CF956660.1|CF956660
EST:     TCATGGC-TTGGATCTTCCTCATGGTGGACATCTTTCTCACGGCTACCAG                         ACTGATACTAAGAAGATTTCAGCAGTTTCGATATTCTTTGAGACAATGCCC
genomic: TCATGGCTTTGGATCTTCCTCATGGTGGACATCTTTCTCACGGCTACCAGgtacatgggt ... atggttgcagACTGATACTAAGAAGATTTCAGCAGTTTCGATATTCTTTGAGACAATGCCC
EST: gi|58661735|gb|CK050415.1|CK050415
EST:     TCATGGCTTTGGATCTTCCTCATGGTGGACATCTTTCTCACGGCTACCAG                         ACTGATACTAAGAAGATTTCAGCAGTTTCGATATTCTTTGAGACAATGCCC
genomic: TCATGGCTTTGGATCTTCCTCATGGTGGACATCTTTCTCACGGCTACCAGgtacatgggt ... atggttgcagACTGATACTAAGAAGATTTCAGCAGTTTCGATATTCTTTGAGACAATGCCC
EST: gi|58691585|gb|CK080272.1|CK080272
EST:     TCATGGCTTTGGATCTTCCTCATGGTGGACATCTTTCTCACGGCTACCAG                         ACTGATACTAAGAAGATTTCAGCAGTTTCGATATTCTTTGAGACAATGCCC
genomic: TCATGGCTTTGGATCTTCCTCATGGTGGACATCTTTCTCACGGCTACCAGgtacatgggt ... atggttgcagACTGATACTAAGAAGATTTCAGCAGTTTCGATATTCTTTGAGACAATGCCC
EST: gi|29681406|gb|CB677681.1|CB677681
EST:     TCATGGCTTTGGATCTTCCTCATGGTGGACATCTTTCTCACGGCTACCAG                         ACTGATACTAAGAAGATTTCAGCAGTTTCGATATTCTTTGAGACAATGCCC
genomic: TCATGGCTTTGGATCTTCCTCATGGTGGACATCTTTCTCACGGCTACCAGgtacatgggt ... atggttgcagACTGATACTAAGAAGATTTCAGCAGTTTCGATATTCTTTGAGACAATGCCC
EST: gi|14571290|gb|BI118658.1|BI118658
EST:     TCATGGCTTTGGATCTTCCTCATGGTGGACATCTTTCTCACGGCTACCAG                         ACTGATACTAAGAAGATTTCAGCAGTTTCGATATTCTTTGAGACAATGCCC
genomic: TCATGGCTTTGGATCTTCCTCATGGTGGACATCTTTCTCACGGCTACCAGgtacatgggt ... atggttgcagACTGATACTAAGAAGATTTCAGCAGTTTCGATATTCTTTGAGACAATGCCC
EST: gi|38472219|gb|CF956350.1|CF956350
EST:     TCATGGCTTTGGATCTTCCTCATGGTGGACATCTTTCTCACGGCTACCAG                         ACTGATACTAAGAAGATTTCAGCAGTTTCGATATTCTTTGAGACAATGCCC
genomic: TCATGGCTTTGGATCTTCCTCATGGTGGACATCTTTCTCACGGCTACCAGgtacatgggt ... atggttgcagACTGATACTAAGAAGATTTCAGCAGTTTCGATATTCTTTGAGACAATGCCC
EST: gi|29674038|gb|CB670313.1|CB670313
EST:     TCATGGCTTTGGATCTTCCTCATGGTGGACATCTTTCTCACGGCTACCAG                         ACTGATACTAAGAAGATTTCAGCAGTTTCGATATTCTTTGAGACAATGCCC
genomic: TCATGGCTTTGGATCTTCCTCATGGTGGACATCTTTCTCACGGCTACCAGgtacatgggt ... atggttgcagACTGATACTAAGAAGATTTCAGCAGTTTCGATATTCTTTGAGACAATGCCC
EST: gi|33800499|gb|CF326119.1|CF326119
EST:     TCATGGCTTTGGATCTTCCTCATGGTGGACATCTTTCTCACGGCTACCAG                         ACTGATACTAAGAAGATTTCAGCAGTTTCGATATTCTTTGAGACAATGCCC
genomic: TCATGGCTTTGGATCTTCCTCATGGTGGACATCTTTCTCACGGCTACCAGgtacatgggt ... atggttgcagACTGATACTAAGAAGATTTCAGCAGTTTCGATATTCTTTGAGACAATGCCC
EST: gi|29681405|gb|CB677680.1|CB677680
EST:     TCATGGCTTTGGATCTTCCTCATGGTGGACATCTTTCTCACGGCTACCAG                         ACTGATACTAAGAAGATTTCAGCAGTTTCGATATTCTTTGAGACAATGCCC
genomic: TCATGGCTTTGGATCTTCCTCATGGTGGACATCTTTCTCACGGCTACCAGgtacatgggt ... atggttgcagACTGATACTAAGAAGATTTCAGCAGTTTCGATATTCTTTGAGACAATGCCC
EST: gi|38471655|gb|CF955786.1|CF955786
EST:     CTTCCTCATGGTGGACATCTTTCTCACGGCTACCAG                         ACTGATACTAAGAAGATTTCAGCAGTTTCGATATTCTTTGAGACAATGCCC
genomic: CTTCCTCATGGTGGACATCTTTCTCACGGCTACCAGgtacatgggt ... atggttgcagACTGATACTAAGAAGATTTCAGCAGTTTCGATATTCTTTGAGACAATGCCC
EST: gi|29672938|gb|CB669213.1|CB669213
EST:     TCATGGCTTTGGATCTTCCTCATGGTGGACATCTTTCTCACGGCTACCAG                         ACTGATACTAAGAAGATTTCAGCAGTTTCGATATTCTTTGAGACAATGCCC
genomic: TCATGGCTTTGGATCTTCCTCATGGTGGACATCTTTCTCACGGCTACCAGgtacatgggt ... atggttgcagACTGATACTAAGAAGATTTCAGCAGTTTCGATATTCTTTGAGACAATGCCC
EST: gi|84117692|gb|CD285458.1|CD285458
EST:     TCATGGCTTTGGATCTTCCTCATGGTGGACATCTTTCTCACGGCTACCAG                         ACTGATACTAAGAAGATTTCAGCAGTTTCGATATTCTTTGAGACAATGCCC
genomic: TCATGGCTTTGGATCTTCCTCATGGTGGACATCTTTCTCACGGCTACCAGgtacatgggt ... atggttgcagACTGATACTAAGAAGATTTCAGCAGTTTCGATATTCTTTGAGACAATGCCC
EST: gi|33381615|gb|CF196958.1|CF196958
EST:     TCATGGCTTTGGATCTTCCTCATGGTGGACATCTTTCTCACGGCTACCAG                         ACTGATACTAAGAAGATTTCAGCAGTTTCGATATTCTTTGAGACAATGCCC
genomic: TCATGGCTTTGGATCTTCCTCATGGTGGACATCTTTCTCACGGCTACCAGgtacatgggt ... atggttgcagACTGATACTAAGAAGATTTCAGCAGTTTCGATATTCTTTGAGACAATGCCC
EST: gi|4714773|gb|AU055890.1|AU055890
EST:     TCATGGCTTTGGATCTTCCTCATGGTGGACATCTTTCTCACGGCTACCAG                         ACTGATACTAAGAAGATTTCAGCAGTTTCGATATTCTTTGAGACAATGCCC
genomic: TCATGGCTTTGGATCTTCCTCATGGTGGACATCTTTCTCACGGCTACCAGgtacatgggt ... atggttgcagACTGATACTAAGAAGATTTCAGCAGTTTCGATATTCTTTGAGACAATGCCC
EST: gi|88413328|gb|CI581343.1|CI581343
EST:     TCATGGCTTTGGATCTTCCTCATGGTGGACATCTTTCTCACGGCTACCAG                         ACTGATACTAAGAAGATTTCAGCAGTTTCGATATTCTTTGAGACAATGCCC
genomic: TCATGGCTTTGGATCTTCCTCATGGTGGACATCTTTCTCACGGCTACCAGgtacatgggt ... atggttgcagACTGATACTAAGAAGATTTCAGCAGTTTCGATATTCTTTGAGACAATGCCC
EST: gi|29674139|gb|CB670414.1|CB670414
EST:     TCATGGCTTTGGATCTTCCTCATGGTGGACATCTTTCTCACGGCTACCAG                         ACTGATACTAAGAAGATTTCAGCAGTTTCGATATTCTTTGAGACAATGCCC
genomic: TCATGGCTTTGGATCTTCCTCATGGTGGACATCTTTCTCACGGCTACCAGgtacatgggt ... atggttgcagACTGATACTAAGAAGATTTCAGCAGTTTCGATATTCTTTGAGACAATGCCC
EST: gi|58692794|gb|CK081481.1|CK081481
EST:     TCATGGCTTTGGATCTTCCTCATGGTGGACATCTTTCTCACGGCTACCAG                         ACTGATACTAAGAAGATTTCAGCAGTTTCGATATTCTTTGAGACAATGCCC
genomic: TCATGGCTTTGGATCTTCCTCATGGTGGACATCTTTCTCACGGCTACCAGgtacatgggt ... atggttgcagACTGATACTAAGAAGATTTCAGCAGTTTCGATATTCTTTGAGACAATGCCC
EST: gi|58609394|gb|CK037427.1|CK037427
EST:     TCATGGCTTTGGATCTTCCTCATGGTGGACATCTTTCTCACGGCTACCAG                         ACTGATACTAAGAAGATTTCAGCAGTTTCGATATTCTTTGAGACAATGCCC
genomic: TCATGGCTTTGGATCTTCCTCATGGTGGACATCTTTCTCACGGCTACCAGgtacatgggt ... atggttgcagACTGATACTAAGAAGATTTCAGCAGTTTCGATATTCTTTGAGACAATGCCC
EST: gi|11442623|gb|BF430526.1|BF430526
EST:     TCATGGCTTTGGATCTTCCTCATGGTGGACATCTTTCTCACGGCTACCAG                         ACTGATACTAAGAAGATTTCAGCAGTTTCGATATTCTTTGAGACAATGCCC
genomic: TCATGGCTTTGGATCTTCCTCATGGTGGACATCTTTCTCACGGCTACCAGgtacatgggt ... atggttgcagACTGATACTAAGAAGATTTCAGCAGTTTCGATATTCTTTGAGACAATGCCC

RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 1 RNA-Seqlibrary.


Block sizes: 75 (upstream exon), 74 (downstream exon)
Score: 270

ACCTGCCAACTTCCATGTTTACACTGCCCTATTGAAACCACATGAGAGAATCATGGCTTTGGATCTTCCTCATGGTGGACATCTTTCTCACGGCTACCAGgtacatgggt ... atggttgcagACTGATACTAAGAAGATTTCAGCAGTTTCGATATTCTTTGAGACAATGCCCTACAGATTGGATGAAAGCACTGGCTTGATTGATTATGATCAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcttggtactctcatcctcccatggcttagttgttcaacttcttgatggttgcagACTGATACTAAGAAGATTTCAGCAGTTTCGATATTCTTTGAGACAATGCCCTACAGATTGGATGAAAGCACTGGCTTGATTGATTATGATCAG
                                        tcttgat  putative branch site (score: 270)
















Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tgagtttcttccccctcaattcttagttatgttcagatataatgctcttggtactctcatcctcccatggcttagttgttcaacttcttgatggttgcagACTGATACTAAGAAGATTTCAGCAGTTTCGATATTCTTTGAGACAATGCCCTACAGATTGGATGAAAGCACTGGCTTGATTGATTATGATCAG

- - - - - - - - - - - - - ttatgtt
- - - - - - - - - - - - - - - - - - - - aatgctc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -cttcttg