Sequence
atgc intronic sequence ATGC exonic sequencegttgagaatttcgtgcagtttttattacctggtggcttctactgcctgcttcgtgcacattatgacaatccagGTGGTAGCAGAACGTGAGCAGAAAATTCAGACAGAGGTGAAAGAAATACGAAAGGTGTTCTATTGTGAGCTCTGCAACAAGCAATACAAACTGGCTATGG
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: Vv14s0060g00320.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: LOC_Os04g02500.2 (Oryza sativa), 3'ss of exon 3
-------------------------------gttgagaatttcgtgcagtttttattacctggtggcttctactgcctgcttcgtgcacattatgacaatccagGTGGTAGCAGAACGTGAGCAGAAAATTCAGACAGAGGTGAAAGAAATACGAAAGGTGTTCTATTGTGAGCTCTGCAACAAGCAATACAAACTGGC-TATGG
||||| |||| | ||| |||||||| |||||| |||| | ||||||| ||||| || |||||||||||||| |||||||||| ||||||||||| | | ||||| || || |||| |||||||||| ||| ||||| |||||||| |||||| |||| |||
gcaagagttgctagcatcagccctcatgatccttgagcattttgggcattttttatt---tggtgg-ttctttttcctgcttggtgcaaatcatgacaatccagGTCATAGCAGAACGCGAGCAGAAAATACGTAGTGAGGTCAAGGAGATACAGAAGGTGTTCTTTTGCAGTCTCTGTAACAAGCAGTACAAATTGGCGCATG-
upper sequence: Vv14s0060g00320.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: LOC_Os04g02500.5 (Oryza sativa), 3'ss of exon 1
---------------------gttgagaatttcgtgcagtttttattacctggtggcttctactgcctgcttcgtgcacattatgacaatccagGTGGTAGCAGAACGTGAGCAGAAAATTCAGACAGAGGTGAAAGAAATACGAAAGGTGTTCTATTGTGAGCTCTGCAACAAGCAATACAAACTGGC-TATGG---------
||||| |||| | ||| |||||||| |||||| |||| | ||||||| ||||| || |||||||||||||| |||||||||| ||||||||||| | | ||||| || || |||| |||||||||| ||| ||||| |||||||| |||||| |||| |||
ctagcatcagccctcatgatccttgagcattttgggcattttttatt---tggtgg-ttctttttcctgcttggtgcaaatcatgacaatccaggtcatagcagAACGCGAGCAGAAAATACGTAGTGAGGTCAAGGAGATACAGAAGGTGTTCTTTTGCAGTCTCTGTAACAAGCAGTACAAATTGGCGCATGAATTTGAGTC
upper sequence: Vv14s0060g00320.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GRMZM2G075551_T03 (Zea mays), 3'ss of exon 3
------------------------------gttgagaatttcgtgcagtttttattacctggtggcttctactgcctgcttcgtgcacattatgacaatccagGTGGTAGCAGAACGTGAGCAGAAAATTCAGACAGAGGTGAAAGAAATACGAAAGGTGTTCTATTGTGAGCTCTGCAACAAGCAATACAAACTGGCT-ATGG
|| || |||| |||| |||||||| |||||| |||| | ||||||| ||||| || |||||||||||||| ||||||| |||||||| ||||| | | || || || || |||| |||||||||| ||| | |||||||| ||||| ||||| |||||| |||
gaggatagctagcatcaaccattaaagagtcttcagcattttgtgcgctttttatt---tggtggtttcttttccctgcttggtgcaaatcatgacaatccagGTCATAGCAGAGCGTGAGCACAAAATCCGCAGTGAAGTCAAGGAGATACAGAAGGTGTTCTTTTGCAACCTCTGCAATAAGCAGTACAAGCTGGCTCATG-
upper sequence: Vv14s0060g00320.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GRMZM2G075551_T02 (Zea mays), 3'ss of exon 3
--------------------gttgagaatttcgtgcagtttttattacctggtggcttctactgcctgcttcgtgcacattatgacaatccagGTGGTAGCAGAACGTGAGCAGAAAATTCAGACAGAGGTGAAAGAAATACGAAAGGTGTTCTATTGTGAGCTCTGCAACAAGCAATACAAACTGGCT-ATGG---------
|| || |||| |||| |||||||| |||||| |||| | ||||||| ||||| || |||||||||||||| ||||||| |||||||| ||||| | | || || || || |||| |||||||||| ||| | |||||||| ||||| ||||| |||||| |||
agcatcaaccattaaagagtcttcagcattttgtgcgctttttatt---tggtggtttcttttccctgcttggtgcaaatcatgacaatccaggtcatagcagAGCGTGAGCACAAAATCCGCAGTGAAGTCAAGGAGATACAGAAGGTGTTCTTTTGCAACCTCTGCAATAAGCAGTACAAGCTGGCTCATGAATTTGAGAG
upper sequence: Vv14s0060g00320.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA19G41310.1 (Glycine max), 3'ss of exon 4
---------------------------gttgagaatttcgtgcagtttttattacctggtggcttctactgcctgcttcgtgcacattatgacaatccagGTGGTAGCAGAACGTGAGCAGAAAATTCAGACAGAGGTGAAAGAAATACGAAAGGTGTTCTATTGTGAGCTCTGCAACAAGCAATACAAACTGGCTATGG
||||||||||| ||||||||||||||||||||||||||| |||||||||||||||||||||||| ||| ||||| |||| ||||||||||| |||||||| || || ||||||||||| |||||||||||||||||||| ||||||||||||||||||||| |||| ||||
cataaggaatcatcaactttggaaggtcttgagaatttcctgcagtttttattacctggtggcttcttctgcctgcttcgtgcacattatgaaaattcagGTCTTAGCTGAACGTGAGCAAAAAATTCAAACTGAAGTGAAAGAAATCCGAAAGGTGTTCTATTGTGATCTCTGCAACAAGCAATACAAATTGGCAATGG
upper sequence: Vv14s0060g00320.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA03G38720.1 (Glycine max), 3'ss of exon 4
---------------------------gttgagaatttcgtgcagtttttattacctggtggcttctactgcctgcttcgtgcacattatgacaatccagGTGGTAGCAGAACGTGAGCAGAAAATTCAGACAGAGGTGAAAGAAATACGAAAGGTGTTCTATTGTGAGCTCTGCAACAAGCAATACAAACTGGCTATGG
||||||||||| ||||||||||||||||||||||||||| |||||||||||||||||||||||| ||| |||||| |||| ||||||||||| |||||||| || || ||| ||||||| |||||||||||||||||||| ||||||||||||||||||||| |||| ||||
catatggaatcatcaactttggaaggtcttgagaatttcctgcagtttttattacctggtggcttcttctgcctgcttcgtgcacattatgaaaattcagGTGTTAGCTGAACGTGAGCAAAAAATTCAAACTGAAGTGCAAGAAATCCGAAAGGTGTTCTATTGTGATCTCTGCAACAAGCAATACAAATTGGCAATGG
upper sequence: Vv14s0060g00320.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: AT5G26610.3 (Arabidopsis thaliana), 3'ss of exon 4
-----------------------------------------------------------gttgagaatttcg---tgcagt-ttttattacctggtgg-----cttctactgcctgcttcgtgcacattatgacaatccagGTGGTAGCAGAACGTGAGCAGAAAATTCAGACAGAGGTGAAAGAAATACGAAAGGTGTTCTATTGTGAGCTCTGCAACAAGCAATACAAACTGGCTATGG
| ||||| |||||| |||||||||||||| | |||||||||| ||||||||| |||||||||||||||||| ||||||||||||||||||| || |||| || || |||||||| || || || ||||||||||| || |||| ||| || || | | || ||||
gtatgcgttcaaaacatatttggatatatccttgtcttttgacgggaatatcgtagaggggaaagaataaaaaactgcagtcttttattacctggttggtggctttctactgcccgcttcgtgcccattatgacaatccagGTCCTAGCAGAACGTGAGCAGAAGATCCAGAGCGATGTTAAAGAAATCCGTAAAGTCTTCTATTGTGAACTATGCAGCAAACAGTATAGAACGGTGATGG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tttttattacctggtggcttctactgcctgcttcgtgcacattatgacaatccagGTGGTAGCAGAACGTGAGCAGAAAATTCAGACAGAGGTGAAAGAAATACGAAAGGTGTTCTATTGTGAGCTCTGCAACAAGCAATACAAACTGGCTATGG
acattat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gttgagaatttcgtgcagtttttattacctggtggcttctactgcctgcttcgtgcacattatgacaatccagGTGGTAGCAGAACGTGAGCAGAAAATTCAGACAGAGGTGAAAGAAATACGAAAGGTGTTCTATTGTGAGCTCTGCAACAAGCAATACAAACTGGCTATGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA