Sequence
atgc intronic sequence ATGC exonic sequencegtaatgtgtactatgaacttttcatgcttcttatgaatcgcacaccaagaaaagtttttttttcttcttgtttttatgtgctcaaatatgacatagtttgattgaatttaaagtttgaatcttatcaaatccattttctgattctttagaagtgtcgtgaattttagAGCAATGTGGTTGCCTCTGGTGGCCTTGGCGGGGAGATTTTTATATGGGATATTGAAGCTGCACTAGCTTCAGCTACAAAATGCAATGATCCAATGGATG
Basic information
species | Glycine max |
transcript | GLYMA10G30050.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA10G30050.1 (Glycine max), 3'ss of exon 4
lower sequence: LOC_Os12g06810.2 (Oryza sativa), 3'ss of exon 5
gtaatgtgtactatgaacttttcatgcttcttatgaatcgcacaccaagaaaagtttttttttcttcttgtttttatgtgctcaaatatgacatagtttgattgaatttaaagtttgaatcttatcaaatccattttctgattctttagaagtgtcgtgaattttagAGCAATGTGGTTGCCTCTGGTGGCCTTGGCGGGGAGATTTTTATATGGGATATTGAAGCTGCACTAGCTTCAGCTACAAAATGCAATGATCCAATGGATG
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-------------------------------------------------------------------------gtatattatccagcactatgcttttctgtggaact---actc---attttatcccttttgttttacatgtttttttttattctctgcaatgtagAGCAATATTGTTGCCTCTGGTGGCCTTGGCGGTGAGGTCTTTATATGGGACCTTGATTCTTCTCTTGCTCCTGTGGCCAAATCTGTAGATGCAAAAGAGG
upper sequence: GLYMA10G30050.1 (Glycine max), 3'ss of exon 4
lower sequence: AT3G05090.1 (Arabidopsis thaliana), 3'ss of exon 5
gtaatgtgtactatgaacttttcatgcttcttatgaatcgcacaccaagaaaagtttttttttcttcttgtttttatgtgctcaaatatgacatagtttgattg----aatttaaagtttgaat---cttatcaaatccattttctgattctttagaagtgtcgtgaattttagAGCAATGTGGTTGCCTCTGGTGGCCTTGGCGGGGAGATTTTTATATGGGATATTGAAGCTGCACTAGCTTCAGCTACAAAATGCAATGAT-CCAATGGATG
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------------------------------------gtaatttctcatttgtcatgcttttttctttatagttcccactgaaaaaaattgat-tggtatggtggtgcaagttttgaggatatatgtgcttctcattgtcgcattctgattctatcttgatttcacaacttttagAATAATGTTGTTGCATCTGGTGGCCTTGGTGGGGAGGTTTTTATATGGGATATTGAAGCTGCTTTGTCACCAGTTACCAAACCTAATGACGCTAATGAAG-
upper sequence: GLYMA10G30050.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv14s0030g01350.t01 (Vitis vinifera), 3'ss of exon 5
gtaatgtgtactatgaacttttcatgcttcttatgaatcgcacaccaagaaaagtttttttt-------tcttcttgttt---ttatgtgctcaaatatgacatagtttgattgaatttaaagtttga-atcttatcaaatccattttctgattctttagaagtgtcgtgaattttagAGCAATGTGGTTGCCTCTGGTGGCCTTGGCGGGGAGATTTTTATATGGGATATTGAAGCTGCACTAGCTTCAGCTACAAAATGCAATGATCCAATGGATG
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gtaatttctttgtcaaaattttcatggaa-ttatttactgcatag-atgaagggttcttgtcagtgtaatgctgttatttaagtttcatgttcaa-tttaatggtgcatatttgggggcattgtgtcatattttgtcgttatcattttctgatccttttatagtgtcatgcattttagAGCAATGTTGTTGCCTCTGGTGGCCTTGGTGGGGAGGTTTTTGTATGGGATCTGGAAGCTGCACTAACTCCAGTCTCAAAGTCAAGTGATGCAATGGAGG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gtttgaatcttatcaaatccattttctgattctttagaagtgtcgtgaattttagAGCAATGTGGTTGCCTCTGGTGGCCTTGGCGGGGAGATTTTTATATGGGATATTGAAGCTGCACTAGCTTCAGCTACAAAATGCAATGATCCAATGGATG
ttctgat putative branch site (score: 3)
ttatcaaat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaatgtgtactatgaacttttcatgcttcttatgaatcgcacaccaagaaaagtttttttttcttcttgtttttatgtgctcaaatatgacatagtttgattgaatttaaagtttgaatcttatcaaatccattttctgattctttagaagtgtcgtgaattttagAGCAATGTGGTTGCCTCTGGTGGCCTTGGCGGGGAGATTTTTATATGGGATATTGAAGCTGCACTAGCTTCAGCTACAAAATGCAATGATCCAATGGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TCAGCT