Sequence
atgc intronic sequence ATGC exonic sequencegtaagataaattacaatatttctcaagagtggtgcatttttggctttactaactatgcagtctcccctctccctgtgggccttattatagGTTTTGAAAGTGAAAGAAGAAAGTTTAGTACCAGCAAATCCTGATATCCTTGATGGAGTGGATGACCTCATGCAACTTAGTTATTTAAATGAGCCGTCAG
Basic information
species | Glycine max |
transcript | GLYMA20G00320.1 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA20G00320.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G139583_T02 (Zea mays), 3'ss of exon 2
gtaagataaattaca-atatttctcaagagtggtgcatttttggctttactaactatgcagtctcccctctccctgtgggccttattatagGTTTTGAAAGTGAAAGAAGAAAGTTTAGTACCAGCAAATCCTGATATCCTTGATGGAGTGGATGACCTCATGCAACTTAGTTATTTAAATGAGCCGTCAG
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-----gtaagttgcagatttcttttaagagt----ctgttctataatcactggaagcatggtcatttgaccgccctt---ccctttttaagGTACTGAGATTGAAAACAGAGAGCCTTCAACCTGCAAATCCTGAAATTCTTGATGGAGTGGATGACCTTATGCAGCTAAGTTATCTAAGTGAACCATCAG
upper sequence: GLYMA20G00320.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G113202_T01 (Zea mays), 3'ss of exon 2
gtaagataaattaca-atatttctcaagagtggtgcatttttggctttactaactatgcagtctcccctctccctgtgggccttattatagGTTTTGAAAGTGAAAGAAGAAAGTTTAGTACCAGCAAATCCTGATATCCTTGATGGAGTGGATGACCTCATGCAACTTAGTTATTTAAATGAGCCGTCAG
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-----gtaagttgcagatttctttctaagatagtctgttctataatc-actggaagcatgatcatttgacccccacccttccctttttaagGTACTGAGATTGAAAACCGAGTGTCTACAACCTGCAAATCCTGAAATTCTTGATGGAGTGGATGATCTTATGCAGCTAAGTTATCTAAGTGAACCATCAG
upper sequence: GLYMA20G00320.1 (Glycine max), 3'ss of exon 3
lower sequence: AT3G19960.2 (Arabidopsis thaliana), 3'ss of exon 3
gtaagataaattacaatatttctcaagagtggtgcatttttggctttactaactatgcagtctcccctctccctgtgggccttattatagGTTTTGAAAGTGAAAGAAGAAAGTTTAGTACCAGCAAATCCTGATATCCTTGATGGAGTGGATGACCTCATGCAACTTAGTTATTTAAATGAGCCGTCAG
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gtaag-taactttttgtatttct--aaggtagc-caggttaatttttg--aagtatttgatctgaaactactttc--aaacttgaaacagGTTATAAAAGTCATATCAGAGACTCTAGTACCTGCAAATCCTGATATTCTTGATGGAGTGGACGATCTTATGCAGCTTAGTTACTTAAATGAGCCATCAG
upper sequence: GLYMA20G00320.1 (Glycine max), 3'ss of exon 3
lower sequence: AT1G50360.1 (Arabidopsis thaliana), 3'ss of exon 3
gtaagataaattacaatatttctcaagagtg-gtgcatttttggctttactaactatgcagtctcccctctccctgtgggccttattatagGTTTTGAAAGTGAAAGAAGAAAGTTTAGTACCAGCAAATCCTGATATCCTTGATGGAGTGGATGACCTCATGCAACTTAGTTATTTAAATGAGCCGTCAG
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gtaagtgattttgttaaattccctgggtgaatgtaaactattattgtaagtgtttgatcggaaacta-tctcttcacttgattca--acagGTTTTAAAAGTCAAATCAGAGACTTTAGTACCTGCAAATCCTGATATTCTTGATGGAGTAGACGATCTCATGCAACTAAGTTATTTAAATGAGCCAGCAG
upper sequence: GLYMA20G00320.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv10s0071g00210.t01 (Vitis vinifera), 3'ss of exon 2
gtaagataaattacaatatttctcaagagtggtgcatttttggctttactaactatgcagtctcccctctccctgtgggcctta-ttatagGTTTTGAAAGTGAAAGAAGAAAGTTTAGTACCAGCAAATCCTGATATCCTTGATGGAGTGGATGACCTCATGCAACTTAGTTATTTAAATGAGCCGTCAG
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gtaag-taaactaatgcaaacttggatgattgattgtatgtcaatgaatctgttgtttacctttttattttgcactggttttcaattttagGTTTTAAAGGTGAATACTGACAGCCTGTTACCTGCAAACCCCGATATACTTGACGGTGTAGATGACCTTATGCAACTTAGTTACTTAAATGAGCCATCGG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.atttttggctttactaactatgcagtctcccctctccctgtgggccttattatagGTTTTGAAAGTGAAAGAAGAAAGTTTAGTACCAGCAAATCCTGATATCCTTGATGGAGTGGATGACCTCATGCAACTTAGTTATTTAAATGAGCCGTCAG
tactaac putative branch site (score: 0)
ccttatt putative PPT
ttattata 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaagataaattacaatatttctcaagagtggtgcatttttggctttactaactatgcagtctcccctctccctgtgggccttattatagGTTTTGAAAGTGAAAGAAGAAAGTTTAGTACCAGCAAATCCTGATATCCTTGATGGAGTGGATGACCTCATGCAACTTAGTTATTTAAATGAGCCGTCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGTGGA