Sequence
atgc intronic sequence ATGC exonic sequence...ccctttgtactgatgtgcattctggtaagatatgttgaatttcaatattcaactactcgtattttaaatttttaatctctctctctctctctcattgcagATGAACATGATTAAAGTTTCCAATATTATGGGTGTTGATCCAAAACCATTTGATCCTAAAACATATGTGGAAGAGGATACTTTTGTAACCGATGAATCTG
Basic information
species | Glycine max |
transcript | GLYMA06G21900.2 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA06G21900.2 (Glycine max), 3'ss of exon 4
lower sequence: LOC_Os03g54930.1 (Oryza sativa), 3'ss of exon 4
ccctttgtactgatgtgcattctggtaagatatg--ttgaatttcaatat-tcaactactcgtattttaaatttttaatctctctctctctctctcattgcagATGAACATGATTAAAGTTTCCAATATTATGGGTGTTGATCCAAAACCATTTGATCCTAAAACATATGTGGAAGAGGATACTTTTGTAACCGATGAATCTG---
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--gtttgcaataatacctgttttataagctcgtgatttttttttcagcaccttgtaggcttgtacaaatagaattttctttctgattgggtttcttttt-tagATGAATGTGATCAAGGTTTCAAATATTATGGGGGTTAATCCAAAACCTTTTGATCCTGAAACATATGTGGAGGAGGATGCTTT---GACAGATGAATCTGGGA
upper sequence: GLYMA06G21900.2 (Glycine max), 3'ss of exon 4
lower sequence: LOC_Os12g38970.1 (Oryza sativa), 3'ss of exon 4
------ccctttgtactgatgtgcattctggtaagatatgttgaatttcaatattcaactactcgtattttaaatttttaatctctctctctctctctcattgcagATGAACATGATTAAAGTTTCCAATATTATGGGTGTTGATCCAAAACCATTTGATCCTAAAACATATGTGGAAGAGGATACTTTTGTAACCGATGAATCTG
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taggctttactaggaatgttatgatcgatgcttaaatgtttttgtgct---tttgcagctattcatatggttatttgttactgactaatttcttaact---tgtagATGAATGTGATCAAGGTATCAAATATTATGGGGATTGACCCAAAGCCTTTTGATCCTAAAACATATGTGGAGGAGGATGTATTTGTTACAGATGAATCTG
upper sequence: GLYMA06G21900.2 (Glycine max), 3'ss of exon 4
lower sequence: LOC_Os07g01880.1 (Oryza sativa), 3'ss of exon 4
ccctttgtactga-tgtgcattctggtaagatatgttgaatttcaatattcaactactcgtatt--ttaaatttttaatctctctctc-tctctctcattgcagATGAACATGATTAAAGTTTCCAATATTATGGGTGTTGATCCAAAACCATTTGATCCTAAAACATATGTGGAAGAGGATACTTTTGTAACCGATGAATCTG
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----taggcttgactaggaatattaatgattggtgcttaaatattttgtgcttttgcagctattcatagatttttttgttactgactgatttcttaacttgtagATGAATGTGATCAAGGTATCAAACATTATGGGGATTGACCCGAAGCCTTTTGATCCTAAAACATATGTGGAGGAGGATGTATTTGTTACAGATGAATCTG
upper sequence: GLYMA06G21900.2 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G048494_T02 (Zea mays), 3'ss of exon 1
ccctttgtactgatgtgcattctggtaagatatgttgaa---tttcaatattcaactactcgtattttaaatttt-taatctctctctctctctctcattgcagATGAACATGATTAAAGTTTCCAATATTATGGGTGTTGATCCAAAACCATTTGATCCTAAAACATATGTGGAAGAGGATACTTTTGTAACCGATGAATCTG
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--gttaattttggtgatatagcaaacacgttgtgtttagaacttttcatgcttggctag--gaattttattttccatgatcactaactgttttctattttgtagATGAATGTGATCAAGGTATCAAACATTATGGGGATTGACCCTAAACCCTTTGATCCAAAAACATATGTGGAAGAAGATGTTTTTGTTACAGATGAATCTG
upper sequence: GLYMA06G21900.2 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G019879_T02 (Zea mays), 3'ss of exon 4
ccctttgtactgatgtgcattctggtaagatatgttgaatttcaatattcaactactcgtattttaaatttttaatctctctctctctctctcattgcagATGAACATGATTAAAGTTTCCAATATTATGGGTGTTGATCCAAAACCATTTGATCCTAAAACATATGTGGAAGAGGATACTTTTGTAACCGATGAATCTG
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tttcatgcttcactatgaattttatcatccacaattgaaggtttgtgcttctgtagctactctcatattgattgatcattaactgttttctattttgtagATGAATGTGATCAAGGTATCAAATATTATGGGGATTGACCCTAAACCCTTTGATCCAAAAACATATGTAGAAGAAGATGTTTTTGTTACAGATGAATCTG
upper sequence: GLYMA06G21900.2 (Glycine max), 3'ss of exon 4
lower sequence: AT5G61150.2 (Arabidopsis thaliana), 3'ss of exon 4
ccctttgtactgatgtgcattctggtaagatatgttgaatttcaatattcaactactcgtattttaaattttta---atctctctctctctctctcattgcagATGAACATGATTAAAGTTTCCAATATTATGGGTGTTGATCCAAAACCATTTGATCCTAAAACATATGTGGAAGAGGATACTTTTGTAACCGATGAATCTG
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--atatctgaaaccccattttctagttgtctatctgtagtgaagatgttctg-tagcaaaattgcgcttcctcatataccgttttctctttgatctttttcagATGAACATGATAAAAGTTTCCAATATCATGGGGATTGATCCAAAGCCTTTTGATGCCAAAACATTCGTTGAAGAAGACACATTCATGACAGATGAACCCG
upper sequence: GLYMA06G21900.2 (Glycine max), 3'ss of exon 4
lower sequence: Vv17s0000g07160.t01 (Vitis vinifera), 3'ss of exon 4
ccctttgtactgatgtgcattctggtaagatatgttgaatttcaata-ttcaacta-ctcgtatttt---aaatttttaatctctctctctctctctcattgcagATGAACATGATTAAAGTTTCCAATATTATGGGTGTTGATCCAAAACCATTTGATCCTAAAACATATGTGGAAGAGGATACTTTTGTAACCGATGAATCTG
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---ctaatagtgccttcagatcatctgatacttgtgaaagtctatcaatttatctgtcttgagctgtggcaaaattttaatat-tcaatagtact-ttgttacagATGAACATGATAAAAGTTTCTAATATAATGGGCATTGAACCAAAGCCATTTGACCCTAAAACGTACGTAGAAGAGGACACATTTGTGACAGATGAATCTG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tattcaactactcgtattttaaatttttaatctctctctctctctctcattgcagATGAACATGATTAAAGTTTCCAATATTATGGGTGTTGATCCAAAACCATTTGATCCTAAAACATATGTGGAAGAGGATACTTTTGTAACCGATGAATCTG
ttttaat putative branch site (score: 3)
tttttaatctctctct CT-rich tract
tactcgtattttaaat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ccctttgtactgatgtgcattctggtaagatatgttgaatttcaatattcaactactcgtattttaaatttttaatctctctctctctctctcattgcagATGAACATGATTAAAGTTTCCAATATTATGGGTGTTGATCCAAAACCATTTGATCCTAAAACATATGTGGAAGAGGATACTTTTGTAACCGATGAATCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAT