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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtatcagaaatcatctccctttggctgacttgatatactggatgtcttcacaatgttatatgatttttggaactgaaactgggcttctcaatttacagTCAATAGATGGCCTTTACTGTGTTGGTGACAGCTGTTTTCCCGGACAAGGTGTAATAGCTGTAGCATTCTCAGGGATCATGTGCGCTCACCGAGTCGCTG

Basic information

species Zea mays
transcript GRMZM2G108457_T02
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G108457_T02 (Zea mays), 3'ss of exon 11
lower sequence: LOC_Os11g36440.1 (Oryza sativa), 3'ss of exon 11
gtaagtatcagaaatcatctccctttggctgacttgatatactggatgtcttcacaatgttatatgatttttggaactgaaactgggcttctcaatttacagTCAATAGATGGCCTTTACTGTGTTGGTGACAGCTGTTTTCCCGGACAAGGTGTAATAGCTGTAGCATTCTCAGGGATCATGTGCGCTCACCGAGTCGCTG
           || | |     | |||  ||||||||| | ||| |  |||||    || |  |  ||| ||||| |||||| |   || || | ||||||||||||||||||| | ||||||||||| |||||||||||||| || ||||||||||| ||||| ||||| |||||||||||||| ||||| ||||| || |
---------gtaagttaatatgcattg-ttgacttgatgtcctgaa-atcttcttg-tgctgcaatattgttgga-ctgaaaatttactgcttattttacagTCAATAGATGGCTTGTACTGTGTTGGCGACAGCTGTTTTCCTGGGCAAGGTGTAATTGCTGTGGCATTTTCAGGGATCATGTGTGCTCATCGAGTTGCAG

upper sequence: GRMZM2G108457_T02 (Zea mays), 3'ss of exon 11
lower sequence: GLYMA10G10990.1 (Glycine max), 3'ss of exon 11
gtaagtatcagaaatcatctccctttggctgacttgatatactggatgtcttcacaatgttatatgat--ttttgg--aactgaaac--tgggcttctcaa-tttacagTCAATAGATGGCCTTTACTGTGTTGGTGACAGCTGTTTTCCCGGACAAGGTGTAATAGCTGTAGCATTCTCAGGGATCATGTGCGCTCACCGAGTCGCTG
||||||  |      ||        |  |||  |   | ||  | |   ||   | ||| | |  ||      ||   |||| || |  |   |   | ||  || |||   |||||||| ||||||||||||||||| ||||| || || ||||||||||| || |||||||| ||||||||  | ||||| ||||| ||||| ||||
gtaagt--ctacttccacaagaaaataactggttcagt-tatggaaacactctgctatgcttttagaaggcactgattaactaaagccataaaccaataaaactttcagGGCATAGATGGTCTTTACTGTGTTGGTGATAGCTGCTTCCCTGGACAAGGTGTTATTGCTGTAGCTTTCTCAGGAGTTATGTGTGCTCATCGAGTAGCTG

upper sequence: GRMZM2G108457_T02 (Zea mays), 3'ss of exon 11
lower sequence: GLYMA02G34060.1 (Glycine max), 3'ss of exon 11
gtaagt--atcagaaatcatctccctttggctgacttgatatactgg-atgtcttcacaatgttatatgatttttggaactgaaactgggcttctcaatttacagTCAATAGATGGCCTTTACTGTGTTGGTGACAGCTGTTTTCCCGGACAAGGTGTAATAGCTGTAGCATTCTCAGGGATCATGTGCGCTCACCGAGTCGCTG
||||||  | || |||  | |    ||  | |      | || |||  |||  || | ||||  ||  ||||   | ||   | |      |    || || |||   |||||||| |||||||||||||| || ||||| || || ||||||||||| || |||||||| ||||||||  | ||||| ||||| ||||| ||||
gtaagtctaccataaacaaacgg--ttcagttatagaaacattctgctatgcttttagaatgcaat--gattaaagtaagccataaacaaataa--aactttcagGGCATAGATGGTCTTTACTGTGTTGGCGATAGCTGCTTCCCTGGACAAGGTGTTATTGCTGTAGCTTTCTCAGGAGTTATGTGTGCTCATCGAGTAGCTG

upper sequence: GRMZM2G108457_T02 (Zea mays), 3'ss of exon 11
lower sequence: Vv08s0032g00800.t01 (Vitis vinifera), 3'ss of exon 11
gtaagtatcagaaatcatctccctttggctgacttgatatactggatgtcttcacaatgtt-atatgatttttggaactgaaac-tgggcttctc-aatttacagTCAATAGATGGCCTTTACTGTGTTGGTGACAGCTGTTTTCCCGGACAAGGTGTAATAGCTGTAGCATTCTCAGGGATCATGTGCGCTCACCGAGTCGCTG
|||||| | |  | | |||      ||| | | |  || ||  |  | | |      | || |  | | |    |||||| | | ||   |  |  || || ||| | ||| |||| || ||||||||||| || ||||| ||||| ||||||||||| ||||||||||| || |||||  | ||||| || |||||||| ||||
gtaagttttacca-taatcagtagatggttaagt--atttagcgattttttatttggtttttagcttagtgaatgaactggatcatgtaatgatggaacttgcagGCTATACATGGTCTCTACTGTGTTGGGGATAGCTGCTTTCCAGGACAAGGTGTTATAGCTGTAGCCTTTTCAGGTGTAATGTGTGCACACCGAGTGGCTG

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|149086468|gb|EE176013.2|EE176013
EST:     TGCCGCGGGGTAAACCCAAGGGCTTACTTGCTATGCCTTTCAATACTACT                         TCAATAGATGGCCTTTACTGTGTTGGTGACAGCTGTTTTCCCGGACAAGGT
genomic: TGCCGCGGGGTAAACCCAAGGGCTTACTTGCTATGCCTTTCAATACTACTgtaagtatca ... caatttacagTCAATAGATGGCCTTTACTGTGTTGGTGACAGCTGTTTTCCCGGACAAGGT
EST: gi|211081518|gb|FL472798.1|FL472798
EST:     TGCCGCGGGGTAAACCCAAGGGCTTACTTGCTATGCCTTTCAATACTACT                         TCAATAGATGGCCTTTACTGTGTTGGTGACAGCTGTTTTCCCGGACAAGGT
genomic: TGCCGCGGGGTAAACCCAAGGGCTTACTTGCTATGCCTTTCAATACTACTgtaagtatca ... caatttacagTCAATAGATGGCCTTTACTGTGTTGGTGACAGCTGTTTTCCCGGACAAGGT
EST: gi|60336973|gb|DN203946.1|DN203946
EST:     TGCCGCGGGGTAAACCCAAGGGCTTACTTGCTATGCCTTTCAATACTACT                         TCAATAGATGGCCTTTACTGTGTTGGTGACAGCTGTTTTCCCGGACAAGGT
genomic: TGCCGCGGGGTAAACCCAAGGGCTTACTTGCTATGCCTTTCAATACTACTgtaagtatca ... caatttacagTCAATAGATGGCCTTTACTGTGTTGGTGACAGCTGTTTTCCCGGACAAGGT
EST: gi|71431774|gb|DR812824.1|DR812824
EST:     TGCCGCGGGGTAAACCCAAGGGCTTACTTGCTATGCCTTTCAATACTACT                         TCAATAGATGGCCTTTACTGTGTTGGTGACAGCTGTTTTCCCGGACAAGGT
genomic: TGCCGCGGGGTAAACCCAAGGGCTTACTTGCTATGCCTTTCAATACTACTgtaagtatca ... caatttacagTCAATAGATGGCCTTTACTGTGTTGGTGACAGCTGTTTTCCCGGACAAGGT
EST: gi|86471657|gb|DY238027.1|DY238027
EST:     TGCCGCGGGGTAAACCCAAGGGCTTACTTGCTATGCCTTTCAATACTACT                         TCAATAGATGGCCTTTACTGTGTTGGTGACAGCTGTTTTCCCGGACAAGGT
genomic: TGCCGCGGGGTAAACCCAAGGGCTTACTTGCTATGCCTTTCAATACTACTgtaagtatca ... caatttacagTCAATAGATGGCCTTTACTGTGTTGGTGACAGCTGTTTTCCCGGACAAGGT

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 4 RNA-Seq libraries.


Block sizes: 48 (upstream exon), 30 (downstream exon)
Score: 32

AAAGACTCACCGGAGATTTCTTGCTCGAAATGATGGTACATATGGACCAATGCCGCGGGGTAAACCCAAGGGCTTACTTGCTATGCCTTTCAATACTACTgtaagtatca ... caatttacagTCAATAGATGGCCTTTACTGTGTTGGTGACAGCTGTTTTCCCGGACAAGGTGTAATAGCTGTAGCATTCTCAGGGATCATGTGCGCTCACCGAGTCGCTG


Block sizes: 48 (upstream exon), 48 (downstream exon)
Score: 96

AAAGACTCACCGGAGATTTCTTGCTCGAAATGATGGTACATATGGACCAATGCCGCGGGGTAAACCCAAGGGCTTACTTGCTATGCCTTTCAATACTACTgtaagtatca ... caatttacagTCAATAGATGGCCTTTACTGTGTTGGTGACAGCTGTTTTCCCGGACAAGGTGTAATAGCTGTAGCATTCTCAGGGATCATGTGCGCTCACCGAGTCGCTG


Block sizes: 48 (upstream exon), 48 (downstream exon)
Score: 51

AAAGACTCACCGGAGATTTCTTGCTCGAAATGATGGTACATATGGACCAATGCCGCGGGGTAAACCCAAGGGCTTACTTGCTATGCCTTTCAATACTACTgtaagtatca ... caatttacagTCAATAGATGGCCTTTACTGTGTTGGTGACAGCTGTTTTCCCGGACAAGGTGTAATAGCTGTAGCATTCTCAGGGATCATGTGCGCTCACCGAGTCGCTG


Block sizes: 48 (upstream exon), 45 (downstream exon)
Score: 58

AAAGACTCACCGGAGATTTCTTGCTCGAAATGATGGTACATATGGACCAATGCCGCGGGGTAAACCCAAGGGCTTACTTGCTATGCCTTTCAATACTACTgtaagtatca ... caatttacagTCAATAGATGGCCTTTACTGTGTTGGTGACAGCTGTTTTCCCGGACAAGGTGTAATAGCTGTAGCATTCTCAGGGATCATGTGCGCTCACCGAGTCGCTG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtcttcacaatgttatatgatttttggaactgaaactgggcttctcaatttacagTCAATAGATGGCCTTTACTGTGTTGGTGACAGCTGTTTTCCCGGACAAGGTGTAATAGCTGTAGCATTCTCAGGGATCATGTGCGCTCACCGAGTCGCTG
                                        cttctc  CT-rich tract
        aatgttatatgatttt  TA-rich tract