Sequence
atgc intronic sequence ATGC exonic sequencegtaattacaatctcttctaagttcatttcataataagatataaccaatttgcttggttgttttcacttttcatgataaatacatacattaccaatgtatcaccctttgttttaactattgtacctgctacaaaagtaaaaaatgttctggttatctgcttaatgtaattgtgcaaatctttgtggcagACAGATTGGGACCTAAGGTTAGCATGCCTTCTCTTATACGCATTTGATTGCGAAGGCAACTTTTGGCAATTGTATGGCGACTTCTTACCGAGTGCAGATG
Basic information
species | Glycine max |
transcript | GLYMA09G05510.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA09G05510.1 (Glycine max), 3'ss of exon 4
lower sequence: LOC_Os05g50980.1 (Oryza sativa), 3'ss of exon 3
gtaattacaatctcttctaagttcatttcataataagatataaccaatttgcttggttgttttcacttttcatgataaatacatacattaccaatgtatcaccctttgttttaactattgtacctgctacaaaag--taaaaaatgttctggttatctgcttaatgtaattgtgcaaatctttgtggcagACAGATTGGGACCTAAGGTTAGCATGCCTTCTCTTATACGCATTTGATTGCGAAGGCAACTTTTGGCAATTGTATGGCGACTTCTTACCGAGTGCAGATG
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-------------------------------------------------------------------------------------tattactcaacacttgcaacctgttttcttcctt-catgcggtgtcaaagcttcataagtgatgtagactgcatcctaacgcaatc-tgta---ccctcttgcagACAGATTGGGATCTAAGGTTAGCTTGCCTTCTTCTCTATGCATTTGATGTAGAAGACAACTTTTGGCAGCTATATGGTGATTTTTTGCCTAGTGTTGATG
upper sequence: GLYMA09G05510.1 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM5G807767_T03 (Zea mays), 3'ss of exon 3
gtaattacaatctcttctaagttcatttcataataagatataaccaatttgcttggttgttttcacttttcatgataaatacatacattaccaatgtatcaccctttgttttaactattgtacctgctacaaaagtaaaaaatgttctggttatctgcttaatgtaattgtgcaaatctttgtggcagACAGATTGGGACCTAAGGTTAGCATGCCTTCTCTTATACGCATTTGATTGCGAAGGCAACTTTTGGCAATTGTATGGCGACTTCTTACCGAGTGCAGATG
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------------------------------------------------------------------------------------acttt-caaaaactcaatcatctgtcttttcttcaacaaatattaaagcgccaataaatgatctatgctggaagctgatgtaatt---tgtattactcttgcagACAGATTGGGATCTAAGATTAGCATGTCTTCTTCTATATGCATTTGATATAGAAGACAACTTTTGGCAGTTATATTCTGATTTTTTGCCAAGTGTTGATG
upper sequence: GLYMA09G05510.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv01s0011g01080.t01 (Vitis vinifera), 3'ss of exon 4
gtaattacaatctcttctaagttcatttcataataagatataaccaatttgcttggttgttttcacttttcatgataaatacatacattaccaatgtatcaccctttgttttaactattgtacctgctacaaaagtaaaaaatgttctggt-tatctgcttaatgtaattgtgcaaatctttgtggcagACAGATTGGGACCTAAGGTTAGCATGCCTTCTCTTATACGCATTTGATTGCGAAGGCAACTTTTGGCAATTGTATGGCGACTTCTTACCGAGTGCAGATG
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--------------------------------------------------------------------------------------ttggttgatgggt-acacaaagttataaatataat-tctgaaatgaagttgatggctctttttgtgtcactggttctta-acttcggtatttgactgtggcagACAGATTGGGATCTGCGGTTAGCATGCCTTCTTTTGTTTGCATTTGATCAAGAGGATAACTTCTGGCAGCTATATGGTGATTTTTTACCTAGTGAAGGAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.agtaaaaaatgttctggttatctgcttaatgtaattgtgcaaatctttgtggcagACAGATTGGGACCTAAGGTTAGCATGCCTTCTCTTATACGCATTTGATTGCGAAGGCAACTTTTGGCAATTGTATGGCGACTTCTTACCGAGTGCAGATG
gcttaat putative branch site (score: 4)
tctttgt putative PPT
ttaatgtaatt TA-rich tract
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaattacaatctcttctaagttcatttcataataagatataaccaatttgcttggttgttttcacttttcatgataaatacatacattaccaatgtatcaccctttgttttaactattgtacctgctacaaaagtaaaaaatgttctggttatctgcttaatgtaattgtgcaaatctttgtggcagACAGATTGGGACCTAAGGTTAGCATGCCTTCTCTTATACGCATTTGATTGCGAAGGCAACTTTTGGCAATTGTATGGCGACTTCTTACCGAGTGCAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGATG