Sequence
atgc intronic sequence ATGC exonic sequence...tcaaagttcttatagcttacattagtgtgataaaatttgttcttatggtctcattagaggtttgtctcattttaaataaggttatgtcatttgttttcagTGTAAGAGCAATAGTTGCTCTAAATCTTCATAGTTATGGAAGTGGAAGAAATCCATGGGGTAATTTGACACCTGAGTATTTAGAGAAG
Basic information
species | Glycine max |
transcript | GLYMA06G30040.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA06G30040.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G073380_T01 (Zea mays), 3'ss of exon 3
----tcaaagttcttatagcttacat---tagtgtg-ataaaatttgttcttatggtctcattagaggtttgtctcattttaaataaggttatgtcatttgttttcagTGTAAGAGCAATAGTTGCTCTAAATCTTCATAGTTATGGAAGTGGAAGAAATCCATGGGGTAATTTGACACCTGAGTATTTAGAGAAG
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aagctcacaatttctctgttttttttggatagcgtacgtagggatcatccttccg--catatagagcgtgaaattaatttcatctgacactctatgatg------cagTGTGAGGGCAATCGTTGCATTAAATCTTCACAATTATGCAAGTGGAAGAAACCCTTGGGGAAATTTGAAGCCTGAATATTTGGAGAAA
upper sequence: GLYMA06G30040.1 (Glycine max), 3'ss of exon 2
lower sequence: AT4G30340.1 (Arabidopsis thaliana), 3'ss of exon 6
tcaaagttcttatagcttacattagtgtgataaaatttgttcttatggtctcattagaggtttgtctcattttaaataaggttatgtcatttgttttcagTGTAAGAGCAATAGTTGCTCTAAATCTTCATAGTTATGGAAGTGGAAGAAATCCATGGGGTAATTTGACACCTGAGTATTTAGAGAAG
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--------------gttcatataaaactaatcttatctttgattaaaactaaaaaaatggcttcacttataatctctctggttttgt--tttggtgt-agCGTAAGATCTATTGTGGTGTTGAATCTTTATAACTATGGAAGTGGAAGACATCCATGGGGTAATCTCAGACCAAAATATTTAGAGAAG
upper sequence: GLYMA06G30040.1 (Glycine max), 3'ss of exon 2
lower sequence: AT5G57690.1 (Arabidopsis thaliana), 3'ss of exon 7
------tcaaagttcttatagcttacattagtgtgataaaatttgttcttatggtctcattagaggtttgtctcattttaaataaggttatgtcatttgtttt--cagTGTAAGAGCAATAGTTGCTCTAAATCTTCATAGTTATGGAAGTGGAAGAAATCCATGGGGTAATTTGACACCTGAGTATTTAGAGAAG
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gtatctacagaatagaaacaaga-acacaaatgagacagaac--actttta-aatctcataattgggtt-tctaatgaaagatgtgtgtttgcttgtttttgggacagTGTAAGAGCAGTTGTTGCATTGAATCTACATAGCTATGGAAGTGGAAGAAACCCTTGGGGAAATCTCAAACAAGATTATCTTGAAAAA
upper sequence: GLYMA06G30040.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv11s0052g01840.t01 (Vitis vinifera), 3'ss of exon 9
-------tcaaagttcttatagcttacattagtgtgataaaatttgttcttatggtctcattagaggtttgtctcattttaaataaggttatgtcatttgttttcagTGTAAGAGCAATAGTTGCTCTAAATCTTCATAGTTATGGAAGTGGAAGAAATCCATGGGGTAATTTGACACCTGAGTATTTAGAGAAG
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caaaatagcaacctttttttattttttatttctttttcttgatttattatta--gtatcatt---tattcatttcatttcacttaatgtttctt--tcaacttcaagTGTGAGGGCAATAGTTGCTTTGAATCTTCATAGCTATGGAAGTGGAAGACATCCATGGGGTAATCTGAAGCCAGACTATTTGGAAAAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tggtctcattagaggtttgtctcattttaaataaggttatgtcatttgttttcagTGTAAGAGCAATAGTTGCTCTAAATCTTCATAGTTATGGAAGTGGAAGAAATCCATGGGGTAATTTGACACCTGAGTATTTAGAGAAG
tttgttttc CT-rich tract
attttaaataaggtta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tcaaagttcttatagcttacattagtgtgataaaatttgttcttatggtctcattagaggtttgtctcattttaaataaggttatgtcatttgttttcagTGTAAGAGCAATAGTTGCTCTAAATCTTCATAGTTATGGAAGTGGAAGAAATCCATGGGGTAATTTGACACCTGAGTATTTAGAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA
- - - - - - - gcttaca
- - - - - - - - - - - tagtgtg
- - - - - - - - - - - - - - - - - - - - -cttatgg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ggttatg