Sequence
atgc intronic sequence ATGC exonic sequence...atcaactgatttgatatcgagatgctgccaatatgcctctaatgtcatgattttagtggctgactaatgaaagtttgcatctttggcatcaacatttcagATTTACTCAAGGACGCCTAATCCTGGACCTAAATTCATAGAGAAGTACAAAGCTTACTTAGCAAACTTTGGGTATGATCCAAGTAAGATCAAGGACACTC
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: Vv19s0177g00320.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: LOC_Os04g53490.1 (Oryza sativa), 3'ss of exon 4
-atcaactgatttgatatcgagatgctgccaatatgcctctaatgtcatgattttagtggctgactaatgaa-agtttgcatc-tttggcatcaacatttcagATTTACTCAAGGACGCCTAATCCTGGACCTAAATTCATAGAGAAGTACAAAGCTTACTTAGCAAACTTTGGGTATGATCCAAGTAAGATCAAGGACACTC
| || | |||| || | |||||||| | || | ||||| |||| || | | ||| || | | | ||| |||||| |||||||| || |||||||||||||| ||||||| ||||||||||| | ||| || ||||| || |||||||| || |||||||||||||| |
gagaaatcaagccaatattccttaccttc--atatgcctattctgacgc-attttgtaaactgaaatatcatcacattgtgtcgtctctcggcaatgcatcagATATACTCAAGAACACCTAATCCTGGACCAGAATTCATCGAGAAGTACAAGTCCTACGCTGCCAACTTCGGTTATGATCCGAGCAAGATCAAGGACACCC
upper sequence: Vv19s0177g00320.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA02G45880.1 (Glycine max), 3'ss of exon 4
-----atcaactgatttgatatcgagatgctgccaatatgcctctaatgtcatgattttagtggctgactaatgaaagtttgcatctttggcatcaacatttcagATTTACTCAAGGACGCCTAATCCTGGACCTAAATTCATAGAGAAGTACAAAGCTTACTTAGCAAACTTTGGGTATGATCCAAGTAAGATCAAGGACACTC
|||| ||||| || | | ||| || || | || ||||||| || || || | ||| | || ||||| || ||||| ||||||||||| ||||| ||||||||| |||| |||||||||||||| ||||| | ||||||| ||| |||||||| || || || || || || |
gctgcatcataagatttataattaata-gctattaactagcatggaagtgtatgattt--gtttttgcttat--agtgttgattcccctgtgatcaatatcacagATATACTCAAGGACACCTAACCCTGGACCTGAATTTATAGAGAAGTACAAGTCTTACCTTGCAAACTATGGATATGATCCTAGCAAAATTAAAGATACGC
upper sequence: Vv19s0177g00320.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA14G02880.1 (Glycine max), 3'ss of exon 4
----atcaactgatttgatatcgagatgctgccaatatgcctctaatgtcatgattttagtggctgactaatgaaagtttgcatctttggcatcaacatttcagATTTACTCAAGGACGCCTAATCCTGGACCTAAATTCATAGAGAAGTACAAAGCTTACTTAGCAAACTTTGGGTATGATCCAAGTAAGATCAAGGACACTC
|||| || || | ||| ||| || | ||| ||||||| | | | || | | ||| || || ||| | || ||||| ||||||||||| ||||| ||||||||| |||| ||| |||||||||| ||||| | ||||||| ||| ||||||||||| || || || || || |
ctgcatcatacagttctttaattaatagctattaattagcatgtaactgtatgatttgatt---ttgcttgt-agtgttgatttccctgtgatctatatcgcagATATACTCAAGGACACCTAACCCTGGACCTGAATTTATACAGAAGTACAAGTCTTACCTTGCAAACTATGGATATGATCCAAGCAAAATTAAAGATACAC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.catgattttagtggctgactaatgaaagtttgcatctttggcatcaacatttcagATTTACTCAAGGACGCCTAATCCTGGACCTAAATTCATAGAGAAGTACAAAGCTTACTTAGCAAACTTTGGGTATGATCCAAGTAAGATCAAGGACACTC
gactaat putative branch site (score: 2)
taatgaaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
atcaactgatttgatatcgagatgctgccaatatgcctctaatgtcatgattttagtggctgactaatgaaagtttgcatctttggcatcaacatttcagATTTACTCAAGGACGCCTAATCCTGGACCTAAATTCATAGAGAAGTACAAAGCTTACTTAGCAAACTTTGGGTATGATCCAAGTAAGATCAAGGACACTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGATCA
- - - - - - - - - - - - ctgccaa
- - - - - - - - - - - - - - - - -tgcctct
- - - - - - - - - - - - - - - - - - - - - - -catgatt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - tggctga
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aatgaaa