Sequence
atgc intronic sequence ATGC exonic sequencegtttcatatgcattttttttttgtgaagtttgagtatgcaattgtagaaagagttcaagtatagcataaacttcttgtgtgttttcttttgtagGTTGTTGAAGATGGATATGAGTTTTTTGCCAATAGACAACTTGTGACTATCTTTTCTGCACCTAACTACTGTGGAGAATTTGACAATGCTGGAGCAATGA
Basic information
species | Glycine max |
transcript | GLYMA10G00960.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA10G00960.1 (Glycine max), 3'ss of exon 2
lower sequence: LOC_Os02g57450.2 (Oryza sativa), 3'ss of exon 2
gtttcatatgcattttttttttgtgaagtttgagtatgcaattgtagaaagagttcaagtatagcataaacttcttgtgtgttttcttttgtagGTTGTTGAAGATGGATATGAGTTTTTTGCCAATAGACAACTTGTGACTATCTTTTCTGCACCTAACTACTGTGGAGAATTTGACAATGCTGGAGCAATGA
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gtgccccatgc-tcacaattacctgacctttttatttttc-ttaccaagtgaattgatttatcagtta---ttcttgccttgttggaatt-cagGTTGTCGAAGATGGGTACGAGTTCTTTGCTAACCGCCAACTTGTAACAATATTCTCGGCCCCTAATTACTGTGGAGAATTTGATAATGCTGGTGCCATGA
upper sequence: GLYMA10G00960.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G390076_T03 (Zea mays), 3'ss of exon 2
gtttcatatgcattttttttttgtgaagtttgagtatgcaattgtagaaagagttcaagtatagcataaacttcttgtgtgttttcttttgtagGTTGTTGAAGATGGATATGAGTTTTTTGCCAATAGACAACTTGTGACTATCTTTTCTGCACCTAACTACTGTGGAGAATTTGACAATGCTGGAGCAATGA
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gttgc---tgtgctctgaaagagtgtgacctacttattcccttataaagtgtatcaaccgtttactcatgtttttgccctgttaaattc---agGTTGTCGAAGATGGATATGAGTTTTTCGCTAGCCGCCAACTCGTAACAATGTTTTCAGCCCCTAACTACTGTGGAGAATTTGATAACGCTGGTGCCATGA
upper sequence: GLYMA10G00960.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G112240_T01 (Zea mays), 3'ss of exon 2
gtttcatatgcattttttttttgtgaagt-ttgagtatgcaattgtagaaagagttcaagtatagcataaactt-cttgtgtgtt-ttcttttgtagGTTGTTGAAGATGGATATGAGTTTTTTGCCAATAGACAACTTGTGACTATCTTTTCTGCACCTAACTACTGTGGAGAATTTGACAATGCTGGAGCAATGA
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-gttgttgtgt-tcttaaagatgtgacctacttattaccttataaactacaaagtgtatcaatagtttacttatgcttttgcattgttgaaattcagGTTGTCGAAGATGGATACGAGTTTTTCGCTAGCCGTCAACTCGTAACAATATTTTCAGCCCCTAACTACTGTGGAGAATTCGACAACGCTGGTGCCATGA
upper sequence: GLYMA10G00960.1 (Glycine max), 3'ss of exon 2
lower sequence: EFJ20637 (Selaginella moellendorffii), 3'ss of exon 2
gtttcatatgcattttttttttgtgaagtttgagtatgcaattgtagaaagagttcaagtatagcataaacttcttgtgtgtttt--cttttgtagGTTGTTGAAGATGGATATGAGTTTTTTGCCAATAGACAACTTGTGACTATCTTTTCTGCACCTAACTACTGTGGAGAATTTGACAATGCTGGAGCAATGA
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--------------------gtatgatgctcgtgagttctttctt---------tctcgt-tgctttgagccccatgtctgcaataacaataacagGTGGTGGAAGACGGATACGAGTTTTTCGCCAACAGACAACTTGTGACGATATTTTCGGCACCCAACTATTGTGGGGAGTTCGACAATTCAGGCGCTATGA
upper sequence: GLYMA10G00960.1 (Glycine max), 3'ss of exon 2
lower sequence: EFJ32796 (Selaginella moellendorffii), 3'ss of exon 2
gtttcatatgcattttttttttgtgaagtttgagtatgcaattgtagaaagagttcaagtatagcataaacttcttgtgtgtttt--cttttgtagGTTGTTGAAGATGGATATGAGTTTTTTGCCAATAGACAACTTGTGACTATCTTTTCTGCACCTAACTACTGTGGAGAATTTGACAATGCTGGAGCAATGA
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--------------------gtatgatgctcgtgagttctttc----------tttattgttgctttgagccccatgtctgcaataacaataacagGTGGTGGAAGACGGATACGAGTTTTTCGCCAACAGACAACTTGTGACGATATTTTCGGCACCCAACTATTGTGGGGAGTTCGACAATTCAGGCGCTATGA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aattgtagaaagagttcaagtatagcataaacttcttgtgtgttttcttttgtagGTTGTTGAAGATGGATATGAGTTTTTTGCCAATAGACAACTTGTGACTATCTTTTCTGCACCTAACTACTGTGGAGAATTTGACAATGCTGGAGCAATGA
tgttttctttt CT-rich tract
ttttctttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtttcatatgcattttttttttgtgaagtttgagtatgcaattgtagaaagagttcaagtatagcataaacttcttgtgtgttttcttttgtagGTTGTTGAAGATGGATATGAGTTTTTTGCCAATAGACAACTTGTGACTATCTTTTCTGCACCTAACTACTGTGGAGAATTTGACAATGCTGGAGCAATGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCA