Sequence
atgc intronic sequence ATGC exonic sequence...aatttcttattaatgcatttatatgtctatgaaagctgagttttactcataatgagaagtgttatgtcaagtgttgagaatttttactagatgtttgcagGCTGTTACTGTTCGTCCGTTATCTTCAGTAACTGCTCTTGTTCGGTTTGCTGAAGAGCCCCAGATGTTTGCAATTGAATTTAGTGATGGATGCCCCATCC
Basic information
species | Glycine max |
transcript | GLYMA05G08040.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA05G08040.1 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G367023_T01 (Zea mays), 3'ss of exon 4
--aatttcttattaatgcatttatatgtctatgaaagctgagttttactcataatgagaagtgtta-tgtcaagtgttgagaatttttactagatg--tttgcagGCTGTTACTGTTCGTCCGTTATCTTCAGTAACTGCTCTTGTTCGGTTTGCTGAAGAGCCCCAGATGTTTGCAATTGAATTTAGTGATGGATGCCCCATCC
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aagataatcagtccttagggtagaatatatataa-----gagactcagctaatatgggccatatgggccttaacacttacttgtttgcactgaatttctttccagGCTGCCATTGTACGACCACTCTCAGCAGTAAGTGCTTTTGTTCGATTTGCTGAAGAGCCACAGATGTTTGCATTTGAATTCAATGATGGCTGCCCAATTC
upper sequence: GLYMA05G08040.1 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G049288_T01 (Zea mays), 3'ss of exon 4
aatttcttattaatgcatttatatgtctatgaaagctgagttttactcataatgagaagtgttatgtcaagtgttgagaatttttactagatgt--ttgcagGCTGTTACTGTTCGTCCGTTATCTTCAGTAACTGCTCTTGTTCGGTTTGCTGAAGAGCCCCAGATGTTTGCAATTGAATTTAGTGATGGATGCCCCATCC
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-----------------------------------------------------------------ataggttcttacttgtttgcactgaatttctttccagGCTGTCATAGTACGACCACTCTCAGCAGTAAGTGCTCTTGTTCGATTTGTAGAAGAACCACAGATATTTGCATTTGAATTCAATGATGGCTGCCCAATTC
upper sequence: GLYMA05G08040.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv11s0016g04420.t01 (Vitis vinifera), 3'ss of exon 4
---aatttcttattaatgcatttatatgtctatgaaagctgagttttactcataatgagaagtgttatgtcaagtgttgagaatttttactagatgtttgcagGCTGTTACTGTTCGTCCGTTATCTTCAGTAACTGCTCTTGTTCGGTTTGCTGAAGAGCCCCAGATGTTTGCAATTGAATTTAGTGATGGATGCCCCATCC
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tttgagttgtgcttaaaaagacattgtgcaaaggatagttatgttt---ctatatgtttgatggttatgtcaagtgttaagaatctcaattagatgtgtgcagGCTGTTATTGTTCGACCTCTATCTGCGGTAAGCTCCCTTGTTCGATTTGCCGAGGAGCCCCAGATGTTTGCAATTGAATTCAATGATGGATGCCCTATTC
upper sequence: GLYMA05G08040.1 (Glycine max), 3'ss of exon 4
lower sequence: PP1S60_221V6.1 (Physcomitrella patens), 3'ss of exon 4
aatttcttattaatgcatttatatgtctatgaaagctgagttttactcataatgagaagtgttatgtcaagtgttgagaatttttactagatgtt--tgcagGCTGTTACTGTTCGTCCGTTATCTTCAGTAACTGCTCTTGTTCGGTTTGCTGAAGAGCCCCAGATGTTTGCAATTGAATTTAGTGATGGATGCCCCATCC
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--ccaaagaaaaaagaaaaagaaaataaagaaaagacaaaatagaaagaaagaaaatcagctcctgcatttctctggaaactaacaaatggttctgtttcagGCGGTCATTGTCCGATCTTTATCTGCGGTGGCTGGTCTTGTTCGGTTTGCTGAGGAACCCCAAATGTTTGCGATTGACTTCAATGATGGTTGCCCTCTTC
upper sequence: GLYMA05G08040.1 (Glycine max), 3'ss of exon 4
lower sequence: EFJ35138 (Selaginella moellendorffii), 3'ss of exon 5
-aatttcttattaat--gcatttatatgtctatgaaagctgagttttactcataatgagaagtgttatgt-caagtgttgagaattt-ttactagatgtttg--cagGCTGTTACTGTTCGTCCGTTATCTTCAGTAACTGCTCTTGTTCGGTTTGCTGAAGAGCCCCAGATGTTTGCAATTGAATTTAGTGATGGATGCCCCATCC
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gtatttctctacagtttgcattcaagcgtgattgtttttttagctttcttcaaaacttgcctgagtgcatgctggtgttaacaggtcattgatggttgatggaacagGCAGTGAGTGGTCGGCCTCTATCGTCAGCAGCAGCTCTCGTTCGATTTGCTGAGGAGCCCCAGATGTTTGCTATTGAGTTTGGTGATGGATGCCCAGTCC
upper sequence: GLYMA05G08040.1 (Glycine max), 3'ss of exon 4
lower sequence: EFJ24089 (Selaginella moellendorffii), 3'ss of exon 5
-aatttcttattaat--gcatttatatgtctatgaaagctgagttttactcataatgagaagtgttatgt-caagtgttgagaattt-ttactagatgtttg--cagGCTGTTACTGTTCGTCCGTTATCTTCAGTAACTGCTCTTGTTCGGTTTGCTGAAGAGCCCCAGATGTTTGCAATTGAATTTAGTGATGGATGCCCCATCC
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gtatttctctacagtttgcattcaagcgtg-attgttttttagctttcttcaaagcttgcctgagtgcatgctgttgttaacaggtcattgatggttgatggaacagGCAGTGAGTGGTCGGCCTCTATCGTCAGTAGCAGCTCTCGTTCGATTTGCTGAGGAGCCCCAGATGTTTGCTATTGAGTTTGGTGATGGATGCCCAGTCC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ctcataatgagaagtgttatgtcaagtgttgagaatttttactagatgtttgcagGCTGTTACTGTTCGTCCGTTATCTTCAGTAACTGCTCTTGTTCGGTTTGCTGAAGAGCCCCAGATGTTTGCAATTGAATTTAGTGATGGATGCCCCATCC
aatttttactagat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
aatttcttattaatgcatttatatgtctatgaaagctgagttttactcataatgagaagtgttatgtcaagtgttgagaatttttactagatgtttgcagGCTGTTACTGTTCGTCCGTTATCTTCAGTAACTGCTCTTGTTCGGTTTGCTGAAGAGCCCCAGATGTTTGCAATTGAATTTAGTGATGGATGCCCCATCC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA