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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgggtttgccaattacgttcttgctattgaattatggccgattgtttgtgaaactggacatttaatttaatttttcagATATTCAATGGCGTGTTCCTGAAAGTCAACAAGGCTACCATTAACATGCTTCGCAGGGTTGAGCCTTATGTTGCATATGG

Basic information

species Zea mays
transcript GRMZM5G868433_T04
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G868433_T02 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os04g51630.3 (Oryza sativa), 3'ss of exon 3
------gtgggtttgccaattacgttcttgc---tattgaa-ttatggccgattgtttgtgaaactggacatttaatttaatttttcagATATTCAATGGCGTGTTCCTGAAAGTCAACAAGGCTACCATTAACATGCTTCGCAGGGTTGAGCCTTATGTTGCATATGG
      |||| |||  |||| |  |   |||   | ||||| |||||    | |  | || ||    |  |   |  |||||||| ||||| || ||||| |||||| |||| |||||||| || |||||||||||||| |||||||||||||| ||||||||||||||
gtgggtgtggttttcacaatcatttgaatgcacgtgttgaaattatgatatagtact-gtcaattgaggaaaaaatgttaattttgcagATCTTTAATGGAGTGTTCTTGAAGGTCAACAAAGCCACCATTAACATGCTGCGCAGGGTTGAGCCATATGTTGCATATGG

upper sequence: GRMZM5G868433_T02 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os08g13690.1 (Oryza sativa), 3'ss of exon 4
gtgggtttgccaatta-cgttcttgctattg----aattatggc---cgattgtttgtgaaactggacattta--atttaatttttcagATATTCAATGGCGTGTTCCTGAAAGTCAACAAGGCTACCATTAACATGCTTCGCAGGGTTGAGCCTTATGTTGCATATGG
|| |||||   ||  |   |||||   | ||    || | | ||   || | || | | ||  | |   || |   ||| ||| | ||||| |||||||| || ||||| || || |||||||| |||||||||||||| |||||||||||||| ||||||||||||||
gttggtttatgaaccagttttcttagaaatgcgtgaactcttgcgtacgctggtgtattaactttgtgcttaattgtttgattctacagATCTTCAATGGTGTCTTCCTCAAGGTTAACAAGGCAACCATTAACATGCTGCGCAGGGTTGAGCCATATGTTGCATATGG

upper sequence: GRMZM5G868433_T02 (Zea mays), 3'ss of exon 4
lower sequence: AT3G13580.2 (Arabidopsis thaliana), 3'ss of exon 4
--gtgggtttgccaattacgttcttgctattgaattatggccgattgtttgtgaa---actggacatttaatttaattttt--cagATATTCAATGGCGTGTTCCTGAAAGTCAACAAGGCTACCATTAACATGCTTCGCAGGGTTGAGCCTTATGTTGCATATGG
       | |    || |     |||  ||    | |     |||       ||    |   |||| ||||  | |||| |  ||||| |||||||| |||||| |||| ||||||||||| |||||||||||||||||| | ||||| || |||||  | |||||
gtaacaatcttatgatgagaactttgtaatatgttaaccaatgatacaaaaggatcgtatctgacacttaaaatcatttattgcagATTTTCAATGGTGTGTTCTTGAAGGTCAACAAGGCAACCATTAACATGCTTCGCCGTGTTGAACCCTATGTAACCTATGG

upper sequence: GRMZM5G868433_T02 (Zea mays), 3'ss of exon 4
lower sequence: AT2G01250.1 (Arabidopsis thaliana), 3'ss of exon 4
---gtgggtttgccaattacg---ttcttgctattgaattatggccga-------ttgtttgtg----aaactggacattta----atttaatttttcagATATTCAATGGCGTGTTCCTGAAAGTCAACAAGGCTACCATTAACATGCTTCGCAGGGTTGAGCCTTATGTTGCATATGG
   || ||||||  |||  |    ||| ||  |  || |  |    ||        | |  |||    | ||||     ||     |||   |  | ||||| |||||||| || ||||| ||||||||||||||||| || |||||||||||| | |||||||| |||||  | || ||
tcagttggtttgataatgtcacatttcatggcaaagactagtatatgaaatgattctatcagtgttgtatactgattgattttggcattgtgtaatgcagATTTTCAATGGTGTTTTCCTTAAAGTCAACAAGGCTACGATGAACATGCTTCGCCGTGTTGAGCCCTATGTCACTTACGG

upper sequence: GRMZM5G868433_T02 (Zea mays), 3'ss of exon 4
lower sequence: Vv09s0054g00140.t01 (Vitis vinifera), 3'ss of exon 2
--------gtgggtttgccaatt-----acgttcttgctattgaattatggccgattgtttg-tgaaactggacatt-taatttaattttt------cagATATTCAATGGCGTGTTCCTGAAAGTCAACAAGGCTACCATTAACATGCTTCGCAGGGTTGAGCCTTATGTTGCATATGG
         || | || | |||      | | | |  |  | |||  ||||    || |||| ||| |   ||  || | ||| | || ||      |||||||||||||| ||||| || ||||| ||||| || || || |||||| | | ||||||||||||||||||  | |||||
ctcttatcatgagcttactaatctaagcaagctatcccattagaaaaatggagtgttctttgatgacataagatcttctcattcacttctttgaatacagATATTCAATGGGGTGTTTCTTAAAGTGAACAAAGCAACAATGAACATGTTGCACAGGGTTGAGCCTTATGTGACTTATGG

upper sequence: GRMZM5G868433_T02 (Zea mays), 3'ss of exon 4
lower sequence: Vv11s0052g00290.t01 (Vitis vinifera), 3'ss of exon 4
--------------------gtgggtttgccaa--ttacgttcttgctattgaattatggccgattgtttgtgaaactggacatttaatttaatttttcagATATTCAATGGCGTGTTCCTGAAAGTCAACAAGGCTACCATTAACATGCTTCGCAGGGTTGAGCCTTATGTTGCATATGG
                     | | | || |||  |||  || |   | ||   |||  |     |  | || |      | | ||  ||||   ||||||||||| ||||| || || |||||||| |||||||| || || || ||||| | ||||||||||||||||||  |||| ||
catgtggttttccttgtgttttagttgtgtcaaagttattttttccttgttaccttacagattcgtagtcgt-atttaaaagaattcttttatggtttcagATATTTAATGGTGTCTTTCTGAAAGTAAACAAGGCAACAATGAATATGCTGCACAGGGTTGAGCCTTATGTGACATACGG

upper sequence: GRMZM5G868433_T02 (Zea mays), 3'ss of exon 4
lower sequence: Vv09s0054g00030.t01 (Vitis vinifera), 3'ss of exon 3
--------gtgggtttgccaatt-----acgttcttgctattgaattatggccgattgtttg-tgaaactggacatt-taatttaattttt------cagATATTCAATGGCGTGTTCCTGAAAGTCAACAAGGCTACCATTAACATGCTTCGCAGGGTTGAGCCTTATGTTGCATATGG
         || | || | |||      | | | |  |  | |||  ||||    || |||| ||| |   ||  || | ||| | || ||      |||||||||||||| ||||| || ||||| ||| | || || || |||||| | | ||||||||||||||||||  | |||||
ctcttatcatgagcttactaatctaagcaagctatcccattagaaaaatggagtgttctttgatgacataagatcttctcattcacttctttgaatacagATATTCAATGGGGTGTTTCTTAAAGTGAACGAAGCAACAATGAACATGTTGCACAGGGTTGAGCCTTATGTGACTTATGG

upper sequence: GRMZM5G868433_T02 (Zea mays), 3'ss of exon 4
lower sequence: Vv09s0054g00060.t01 (Vitis vinifera), 3'ss of exon 3
--------gtgggtttgccaatt-----acgttcttgctattgaattatggccgattgtttg-tgaaactggacatt-taatttaattttt------cagATATTCAATGGCGTGTTCCTGAAAGTCAACAAGGCTACCATTAACATGCTTCGCAGGGTTGAGCCTTATGTTGCATATGG
         || | || | |||      | | | |  |  | |||  ||||    || |||| ||| |   ||  || | ||| | || ||      |||||||||||||| ||||| || ||||| ||||| || || || |||| | | | ||||||||||||||||||  | |||||
ctcttatcatgagcttactaatctaagcaagctatcccattagaaaaatggagtgttctttgatgacataagatcttctcattcacttctttgaatacagATATTCAATGGGGTGTTTCTTAAAGTGAACAAAGCAACAATGAACAAGTTGCACAGGGTTGAGCCTTATGTGACTTATGG

upper sequence: GRMZM5G868433_T02 (Zea mays), 3'ss of exon 4
lower sequence: Vv09s0054g00010.t01 (Vitis vinifera), 3'ss of exon 3
--------gtgggtttgccaatt-----acgttcttgctattgaattatggccgattgtttg-tgaaactggacatt-taatttaattttt------cagATATTCAATGGCGTGTTCCTGAAAGTCAACAAGGCTACCATTAACATGCTTCGCAGGGTTGAGCCTTATGTTGCATATGG
         || | || | |||      | | | |  |  | |||  ||||    || |||| ||| |   |   || | ||| | || ||      |||||||||||||| ||||| || ||||| ||||| || || || |||||| | | ||||||||||||||||||  | |||||
ctcttatcatgagcttactaatctaagcaagctatcccattagaaaaatggagtgttctttgatgatataaggtcttctcattcacttctttgaatacagATATTCAATGGGGTGTTTCTTAAAGTGAACAAAGCAACAATGAACATGTTGCACAGGGTTGAGCCTTATGTGACTTATGG

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|15632349|gb|BI679442.1|BI679442
EST:     CCATGCACCCTAAGACCAGGAAGATATTGCAGCTTCTGCGTTTGAGGCAG                         ATCTTCAATGGCGTGTTCCTGAAAGTCAACAAGGCTACCATTAACATGCTT
genomic: CCATGCATCCTAAGACCAGGAAGATATTGCAGCTTCTGCGTTTGAGGCAGgtgggtttgc ... aatttttcagATATTCAATGGCGTGTTCCTGAAAGTCAACAAGGCTACCATTAACATGCTT
EST: gi|211173109|gb|FK956294.1|FK956294
EST:     CCATGCATCCTAAGACCAGGAAGATATTGCAGCTTCTGCGTTTKAGGCAG                         ATATTCAATGGCGTGTTCCTGAAAGTCAACAAGGCTACCATTAACATGCTT
genomic: CCATGCATCCTAAGACCAGGAAGATATTGCAGCTTCTGCGTTTGAGGCAGgtgggtttgc ... aatttttcagATATTCAATGGCGTGTTCCTGAAAGTCAACAAGGCTACCATTAACATGCTT
EST: gi|94477419|gb|EB706377.1|EB706377
EST:     CCATGCATCCTAAGACCAGGAAGATATTGCAGCTTCTGCGTTTGAGGCAG                         ATATTCAATGGCGTGTTCCTGAAAGTCAACAAGGCTACCATTAACATGCTT
genomic: CCATGCATCCTAAGACCAGGAAGATATTGCAGCTTCTGCGTTTGAGGCAGgtgggtttgc ... aatttttcagATATTCAATGGCGTGTTCCTGAAAGTCAACAAGGCTACCATTAACATGCTT
EST: gi|211173107|gb|FK956292.1|FK956292
EST:     CCATGCACCCTAAGACCAGGAAGATATTGCAGCTTCTGCGTTTGAGGCAG                         ATCTTCAATGGCGTGTTCCTGAAAGTCAACAAGGCTACCATTAACATGCTT
genomic: CCATGCATCCTAAGACCAGGAAGATATTGCAGCTTCTGCGTTTGAGGCAGgtgggtttgc ... aatttttcagATATTCAATGGCGTGTTCCTGAAAGTCAACAAGGCTACCATTAACATGCTT
EST: gi|211171435|gb|FK956283.1|FK956283
EST:     CCATGCACCCTAAGACCAGGAAGATATTGCAGCTTCTGCGTTTGAGGCAG                         ATCTTCAATGGCGTGTTCCTGAAAGTCAACAAGGCTACCATTAACATGCTT
genomic: CCATGCATCCTAAGACCAGGAAGATATTGCAGCTTCTGCGTTTGAGGCAGgtgggtttgc ... aatttttcagATATTCAATGGCGTGTTCCTGAAAGTCAACAAGGCTACCATTAACATGCTT
EST: gi|166438461|gb|EG182561.1|EG182561
EST:     CCATGCATCCTAAGACCAGGAAGATATTGCAGCTTCTGCGTTTGAGGCAG                         ATATTCAATGGCGTGTTCC
genomic: CCATGCATCCTAAGACCAGGAAGATATTGCAGCTTCTGCGTTTGAGGCAGgtgggtttgc ... aatttttcagATATTCAATGGCGTGTTCC
EST: gi|15590144|gb|BI674760.1|BI674760
EST:     CCATGCACCCTAAGACCAGGAAGATATTGCAGCTTCTGCGTTTGAGGCAG                         ATCTTCAATGGCGTGTTCCTGAAAGTCAACAAGGCTACCATTAACATGCTT
genomic: CCATGCATCCTAAGACCAGGAAGATATTGCAGCTTCTGCGTTTGAGGCAGgtgggtttgc ... aatttttcagATATTCAATGGCGTGTTCCTGAAAGTCAACAAGGCTACCATTAACATGCTT
EST: gi|211173119|gb|FK956304.1|FK956304
EST:     CCATGCATCCTAAGACCAGGAAGATATTGCAGCTTCTGCGTTTGAGGCAG                         ATATTCAATGGCGTGTTCCTGAAAGTCAACANG-CTACCATTAACATGCTT
genomic: CCATGCATCCTAAGACCAGGAAGATATTGCAGCTTCTGCGTTTGAGGCAGgtgggtttgc ... aatttttcagATATTCAATGGCGTGTTCCTGAAAGTCAACAAGGCTACCATTAACATGCTT
EST: gi|211171440|gb|FK956288.1|FK956288
EST:     CCATGCACCCTAAGACCAGGAAGATATTGCAGCTTCTGCGTTTGARGCAG                         ATCTTCAATGGCGTGTT
genomic: CCATGCATCCTAAGACCAGGAAGATATTGCAGCTTCTGCGTTTGAGGCAGgtgggtttgc ... aatttttcagATATTCAATGGCGTGTT
EST: gi|211173115|gb|FK956300.1|FK956300
EST:     CCATGCATCCTAAGACCAGGAAGATATTGCAGCTTCTGCGTTTGAGGCAG                         ATATTCAATGGCGTGT
genomic: CCATGCATCCTAAGACCAGGAAGATATTGCAGCTTCTGCGTTTGAGGCAGgtgggtttgc ... aatttttcagATATTCAATGGCGTGT
EST: gi|20299953|gb|BQ162896.1|BQ162896
EST:     CCATGCACCCTAAGACCAGGAAGATATTGCAGCTTCTGCGTTTGAGGCAG                         ATCTTCAATGGAGTGTTCCTGAAAGTCAACAAAGCAACCATTAACATGCTT
genomic: CCATGCATCCTAAGACCAGGAAGATATTGCAGCTTCTGCGTTTGAGGCAGgtgggtttgc ... aatttttcagATATTCAATGGCGTGTTCCTGAAAGTCAACAAGGCTACCATTAACATGCTT
EST: gi|211173112|gb|FK956297.1|FK956297
EST:     CCATGCACCCTAAGACCAGGAAGATATTGCAGCTTCTGCGTTTGAGGCAG                         ATCTTCAATGGCGTGTTCCTGAAAGTCAACAAGGCTACCATTAACATGC
genomic: CCATGCATCCTAAGACCAGGAAGATATTGCAGCTTCTGCGTTTGAGGCAGgtgggtttgc ... aatttttcagATATTCAATGGCGTGTTCCTGAAAGTCAACAAGGCTACCATTAACATGC
EST: gi|9733002|gb|BE511754.1|BE511754
EST:     CCATGCACCCTAAGACCAGGAAGATATTGCAGCTTCTGCGTTTGAGGCAG                         ATCTTCAATGGCGTGTTCCTGAAAGTCAACAAGGCTACCATTAACATGCTT
genomic: CCATGCATCCTAAGACCAGGAAGATATTGCAGCTTCTGCGTTTGAGGCAGgtgggtttgc ... aatttttcagATATTCAATGGCGTGTTCCTGAAAGTCAACAAGGCTACCATTAACATGCTT
EST: gi|15313739|gb|BI478933.1|BI478933
EST:     CCATGCACCCTAAGACCAGGAAGATATTGCAGCTTCTGCGTTTGAGGCAG                         ATCTTCAATGGCGTGTTCCTGAAAGTCAACAAGGCTACCATTAACATGCTT
genomic: CCATGCATCCTAAGACCAGGAAGATATTGCAGCTTCTGCGTTTGAGGCAGgtgggtttgc ... aatttttcagATATTCAATGGCGTGTTCCTGAAAGTCAACAAGGCTACCATTAACATGCTT

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: 49 (upstream exon), 49 (downstream exon)
Score: 1571

TATCAATGCCATGCATCCTAAGACCAGGAAGATATTGCAGCTTCTGCGTTTGAGGCAGgtgggtttgc ... aatttttcagATATTCAATGGCGTGTTCCTGAAAGTCAACAAGGCTACCATTAACATGCTTCGCAGGGTTGAGCCTTATGTTGCATATGG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 1492

TATCAATGCCATGCATCCTAAGACCAGGAAGATATTGCAGCTTCTGCGTTTGAGGCAGgtgggtttgc ... aatttttcagATATTCAATGGCGTGTTCCTGAAAGTCAACAAGGCTACCATTAACATGCTTCGCAGGGTTGAGCCTTATGTTGCATATGG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 1257

TATCAATGCCATGCATCCTAAGACCAGGAAGATATTGCAGCTTCTGCGTTTGAGGCAGgtgggtttgc ... aatttttcagATATTCAATGGCGTGTTCCTGAAAGTCAACAAGGCTACCATTAACATGCTTCGCAGGGTTGAGCCTTATGTTGCATATGG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 841

TATCAATGCCATGCATCCTAAGACCAGGAAGATATTGCAGCTTCTGCGTTTGAGGCAGgtgggtttgc ... aatttttcagATATTCAATGGCGTGTTCCTGAAAGTCAACAAGGCTACCATTAACATGCTTCGCAGGGTTGAGCCTTATGTTGCATATGG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctattgaattatggccgattgtttgtgaaactggacatttaatttaatttttcagATATTCAATGGCGTGTTCCTGAAAGTCAACAAGGCTACCATTAACATGCTTCGCAGGGTTGAGCCTTATGTTGCATATGG
                                         atttaat  putative branch site (score: 841)
                                               tttttc  CT-rich tract
                                  acatttaatttaattt  TA-rich tract