Sequence
atgc intronic sequence ATGC exonic sequence...tcttgtttctagtatgttacacaaaattctagtgctggtctgtggttatgattaatctatggtgaaataacagcatttctttctggcatgtcttttacagATGGCAGATCCTTTGACTGCTTTGATGTATGCAGTACAAGTCATGAATTTTCTCAAGACTCTTGTTGTGAAGGCATTGAGAGAAAGAGAGGAATCTATTG
Basic information
| species | Glycine max |
| transcript | GLYMA19G38120.1 |
| intron # | 4 |
| splice site | 3' |
| intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA19G38120.1 (Glycine max), 3'ss of exon 4
lower sequence: LOC_Os12g05900.1 (Oryza sativa), 3'ss of exon 4
tcttgtttctagtatgttacacaaaattctagtgctggtctgtggttatgattaatctatggtgaaataacagcatttctttctggcatgtcttttacagATGGCAGATCCTTTGACTGCTTTGATGTATGCAGTACAAGTCATGAATTTTCTCAAGACTCTTGTTGTGAAGGCATTGAGAGAAAGAGAGGAATCTATTG
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---------------gtagtgtgttatcctattgc--gatcatggtactgatatttcattaggtggattctaactgttgtc----acacatgtaatgcagATGGCAGATCCCTTGACTGCATTGATGTATGCAGTACAAGTGATGAATTTTCTTAAGATGCTAATACAAAAAACCCTCAAGGATAGAGAAGAGTCTGATC
upper sequence: GLYMA19G38120.1 (Glycine max), 3'ss of exon 4
lower sequence: LOC_Os11g05540.1 (Oryza sativa), 3'ss of exon 4
tcttgtttctagtatgttacacaaaattctagtgctggtctgtggttatgattaatctatggtgaaataacagcatttctttctg-gcatgtcttttacagATGGCAGATCCTTTGACTGCTTTGATGTATGCAGTACAAGTCATGAATTTTCTCAAGACTCTTGTTGTGAAGGCATTGAGAGAAAGAGAGGAATCTATTG
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---------------gtaatgcactgtcctaataataaact-----tatgatt----ttaagtgtggtcgatgcttactgtcatgcacatatgtaatgcagATGTCAGATCCATTGACCGCACTGATGTATGCGGTGCAAGTGATGAATTTTCTCAAGATGCTAATACAGAAGACCCTCAAGGGTAGACAAGAGTCCAATC
upper sequence: GLYMA19G38120.1 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G136069_T01 (Zea mays), 3'ss of exon 3
-----tcttgtttctagtatgttacacaaaattctagtgctggtctgtggttatgattaatctatggtgaaataaca-gcatttctttctggcatgtcttt--tacagATGGCAGATCCTTTGACTGCTTTGATGTATGCAGTACAAGTCATGAATTTTCTCAAGACTCTTGTTGTGAAGGCATTGAGAGAAAGAGAGGAATCTATTG
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gtattgcattgtgctaatattgtagcaattagcaaactagcaatatatacctcaccccgagcagtggaacggttatgcgtgctaactattagcaaacttacaatgcagATGGCAGATCCTTTGACTGCACTGATGTATGCAGTCCAAGTGATGAATTTTCTCAAGATGCTGGTACAAAAGACCCTCAAGGATAGAGAGGAGTCCACTC
upper sequence: GLYMA19G38120.1 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G113073_T01 (Zea mays), 3'ss of exon 4
tcttgtttctagtatgttacacaaaattctagtgctggtctgtggttatgattaatctatggtgaa---ataacagcatttct--ttctggcatgtcttt--tacagATGGCAGATCCTTTGACTGCTTTGATGTATGCAGTACAAGTCATGAATTTTCTCAAGACTCTTGTTGTGAAGGCATTGAGAGAAAGAGAGGAATCTATTG
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--------gtattgcattgtgctga--tacgatagcgattagcaa--actatcaatatatacttcacccatcacaatgatgctaactatagcacgcttacaatgcagATGGCAGATCCTTTGACTGCACTGATGTATGCAGTCCAAGTGATGAATTTTCTCAAGATGCTGGTACAAAAGACCCTCAAGGATAGAGAGGAGTCGACCC
upper sequence: GLYMA19G38120.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv08s0007g03140.t01 (Vitis vinifera), 3'ss of exon 4
-tcttgtttctagtatgtt-acacaaaattctagtgctggtctgtggttatgattaatctatggtgaaataaca-gcatttctttctggcatgtcttttacagATGGCAGATCCTTTGACTGCTTTGATGTATGCAGTACAAGTCATGAATTTTCTCAAGACTCTTGTTGTGAAGGCATTGAGAGAAAGAGAGGAATCTATTG
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atcctcttttaaataaactcactgatgtttttcttattttgatatagttttgtacattctg-gtcaatgtgaggtgcaatgatatct--tctgttggttgcagATGGCAGATCCCTTGACAGCCTTGATGTATGCAGTCCAAGTGATGAATTTTCTCAAGACTTTGATAATCAGGACGCTTAGGGAAAGGGAGGACTCAATAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttatgattaatctatggtgaaataacagcatttctttctggcatgtcttttacagATGGCAGATCCTTTGACTGCTTTGATGTATGCAGTACAAGTCATGAATTTTCTCAAGACTCTTGTTGTGAAGGCATTGAGAGAAAGAGAGGAATCTATTG
aaataac putative branch site (score: 2)
tgtctttt putative PPT
attaatctat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tcttgtttctagtatgttacacaaaattctagtgctggtctgtggttatgattaatctatggtgaaataacagcatttctttctggcatgtcttttacagATGGCAGATCCTTTGACTGCTTTGATGTATGCAGTACAAGTCATGAATTTTCTCAAGACTCTTGTTGTGAAGGCATTGAGAGAAAGAGAGGAATCTATTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA
- - - - - - - - - acacaaa
- - - - - - - - - - - - - - - - tgctggt
- - - - - - - - - - - - - - - - - - - -ctgtggt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - -tatggtg
