Sequence
atgc intronic sequence ATGC exonic sequence...tgcatgggaagaaaagtagataaaaatgaaatacgcaagagattagttggttttgcatttgatccattcttatcgctaccttctttcatatgctttacagACCATCGCCACAGTATGCATGTTCCTCGCAGGGAAGGTTGAAGAGACTCCACGCCCACTGAAGGATGTTATCCTTGTTTCCTATGAAATAATTCATAAAA
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: Vv00s0125g00270.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: LOC_Os12g30020.2 (Oryza sativa), 3'ss of exon 3
---tgcatgggaagaaaagtagataaaaatgaaatac---gcaagagattagttggttttgcatttgatccattcttatcgctaccttctttcatatgctttacagACCATCGCCACAGTATGCATGTTCCTCGCAGGGAAGGTTGAAGAGACTCCACGCCCACTGAAGGATGTTATCCTTGTTTCCTATGAAATAATTCATAAAA
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gattgcatgatcttaattttactcctatgttaagtgttgtcctatagatctgtacctgtttgaagagagaacttataatttgtactgaccgtt------cttacagACAATTGCCACAGTTTGCATGTTCTTGGCTGGAAAAGTTGAAGAGACGCCTAGGCCTTTGAAAGATGTTATTCTGGTTTCTTATGAGATTATTCATAAAA
upper sequence: Vv00s0125g00270.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA20G02880.1 (Glycine max), 3'ss of exon 2
---------tgcatgggaagaaaagtagataaaaatgaaatacgcaagagattagttggttttgcatttgatccattcttatcgctaccttctttcatatgctttacagACCATCGCCACAGTATGCATGTTCCTCGCAGGGAAGGTTGAAGAGACTCCACGCCCACTGAAGGATGTTATCCTTGTTTCCTATGAAATAATTCATAAAA
| || |||| |||||| || | | || | || | || | | | | ||| || | ||| | | | ||| |||||||| || || || || |||||||| || |||||||||||||||||||| || ||||| ||||||||||| |||||||| ||||| || ||||| || |
ttcctaatttatattaagagaatggtagatgttaaagcattat-----aattttaaagattacttaatcaa---aatctcataattcacttgatgaactt-ttttgcagACCATTGCAACGGTCTGTATGTTCCTTGCTGGGAAGGTTGAAGAGACTCCTCGTCCACTAAAGGATGTTATTCTTGTTTCTTATGAGATCATTCACAAGA
upper sequence: Vv00s0125g00270.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA07G35010.1 (Glycine max), 3'ss of exon 2
tgcatgggaagaaaagtagataaaaatgaaatacgcaagagattagt-tggttttgcatttgatccattctta---tcgctaccttctttcatatgctttacagACCATCGCCACAGTATGCATGTTCCTCGCAGGGAAGGTTGAAGAGACTCCACGCCCACTGAAGGATGTTATCCTTGTTTCCTATGAAATAATTCATAAAA
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----aggttcctaatttatattaagagaatgtagatgttaaagctgtatagttttaaagattacttaatcaaaaactcataattcacttgatgaacttttgcagACCATTGCAACGGTCTGTATGTTCCTTGCTGGGAAGGTTGAAGAGACTCCTCGTCCACTAAAGGATGTTATTCTTGTTTCTTATGAGATCATTCACAAGA
upper sequence: Vv00s0125g00270.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: AT5G45190.1 (Arabidopsis thaliana), 3'ss of exon 3
----tgcatgggaagaaaagta-gataaaaatgaaatacgcaagagattagttggttttgcatttgatccattcttatcgctaccttctttcatatgctttacagACCATCGCCACAGTATGCATGTTCCTCGCAGGGAAGGTTGAAGAGACTCCACGCCCACTGAAGGATGTTATCCTTGTTTCCTATGAAATAATTCATAAAA
|||| || || | ||| | | | | |||| | | | |||| | || | | || |||| | | | | |||||||| || || |||||||||||||| || || |||||||| || |||||||| || |||| |||||||| |||| |||||||| || || | || |
tctatgcagaattagtgaattgtgattgttgttatttcttctagagcggaaaaaaatactcg---gatctttactgagctctctcttcat--gttgtttctgcagACCATTGCAACTGTATGCATGTTCCTTGCTGGAAAGGTTGAGGAAACTCCACGGCCCTTGAAAGATGTTATTTTTGTCTCCTATGAGATTATAAACAAGA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gttggttttgcatttgatccattcttatcgctaccttctttcatatgctttacagACCATCGCCACAGTATGCATGTTCCTCGCAGGGAAGGTTGAAGAGACTCCACGCCCACTGAAGGATGTTATCCTTGTTTCCTATGAAATAATTCATAAAA
atttgat putative branch site (score: 5)
attcttat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tgcatgggaagaaaagtagataaaaatgaaatacgcaagagattagttggttttgcatttgatccattcttatcgctaccttctttcatatgctttacagACCATCGCCACAGTATGCATGTTCCTCGCAGGGAAGGTTGAAGAGACTCCACGCCCACTGAAGGATGTTATCCTTGTTTCCTATGAAATAATTCATAAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGATG
-gcatggg
- - - - aagaaaa
- - - - - - - - - -ataaaaa
- - - - - - - - - - - - - -gaaatac
- - - - - - - - - - - - - - - - - -caagaga
- - - - - - - - - - - - - - - - - - - - - -tagttgg
- - - - - - - - - - - - - - - - - - - - - - - - - - - gcatttg