Sequence
atgc intronic sequence ATGC exonic sequence...tttcaccttctttaaaccagcattaggaagttttgctatccattgttcaattaatagtacttatgttcttataaatctcatttgctggattatataccagGCATCTACAGCGACCACAGACACTAGCTGCGAGTCTGTGGTCATGAGCGGTCAGCACCAACAACAGCAAAACCCAACACCTCAGCATCCTCAAAGGGATG
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: Vv10s0003g04670.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: LOC_Os12g41860.1 (Oryza sativa), 3'ss of exon 2
tttcaccttctttaaaccagcattaggaagttttgctatccattgttcaattaatagtacttatgttcttataaatctcatttgctggattatataccagGCATCTACAGCGACCACAGACACTAGCTGCGAGTCTGTGGTCATGAGCGGTCAGCACCAACAACAGCAAAACCCAACACCTCAGCATCCTCAAAGGGATG
| | || | | | | || | || || | || || | || | | | || | | |||| | || | || | ||| |||| |||||||| || ||||| ||||||||||| | || ||||||||||| ||||||||||||||| || || |||||| ||||||||||
-gtgagctccctgtgcttacaggcttttgttcttacaattgcttcatattttgatcatcctgttttcttaatcagtaatgtttgtatg--tactttgtagCCTTCTGCAGCCACCACAGATACAAGCTGTGAGTCTGTGGTGACAAGTGGTCAGCACCATCAACAGCAAAACCCAGCAGTTCTGCATCCGCAAAGGGATG
upper sequence: Vv10s0003g04670.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: LOC_Os03g43930.2 (Oryza sativa), 3'ss of exon 2
tttcaccttctttaaaccagcattaggaagt-tttgctatccattgttcaat--taatagtacttatg-ttcttat---aaatctcatttgctg-gattatataccagGCATCTACAGCGACCACAGACACTAGCTGCGAGTCTGTGGTCATGAGCGGTCAGCACCAACAACAGCAAAACCCAACACCTCAGCATCCTCAAAGGGATG
|| ||| || || ||| | | | || ||| | | ||| | || ||| | ||| | | |||| ||| | | ||| | ||| || || |||||||| ||||| ||||||||||| | || ||||| ||||| ||||||||||||||| || | || ||| |||||||| |
--------cctagaaatagattccagtgtgtgtttaatctttttaatttaatgttgttcgtattactggttcctgcctctaatgttgtgtgctatgatgtttttacagCCTTCTGTGGCAACTACAGACACGAGCTGTGAGTCTGTGGTTACAAGTGGTCAACACCACCAACAGCAAAACCCAGCAGCCACGCGTCCGCAAAGGGACG
upper sequence: Vv10s0003g04670.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GRMZM2G023291_T01 (Zea mays), 3'ss of exon 2
-------------------------------------------------------------------------tttcaccttctttaaaccagcattaggaagttttgctatccat---tgttcaattaatagtacttatgttcttataaatctcatttgctggatt---atatac-cagGCATCTACAGCGACCACAGACACTAGCTGCGAGTCTGTGGTCATGAGCGGTCAGCACCAACAACAGCAAAACCCAACACCTCAGCATCCTCAAAGGGATG
| ||| | | | || | | || || | | | | || | | | | | || | ||| || || || |||| ||| | ||| | ||||| |||||||| ||||| ||||||||||||| || ||||||||||| ||||||||||||||| || ||| || ||||||| ||||||
gtgagatccatctcccttgctcattccccagaacatcttatttatatttttttttctagataaatcagctgaatggcacaaagtatcatgtagtagtgaatggtgctgttttatgtaagttttgatgcgaaccttgtcgcatgattccacgtctaataccgtgtgttttgatatttgcagCCTTCTGCTGCGACTACAGACACGAGCTGTGAGTCTGTGGTCACAAGTGGTCAGCACCACCAACAGCAAAACCCAGCAGCTCCGCGTCCTCAACGGGATG
upper sequence: Vv10s0003g04670.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GRMZM2G178102_T01 (Zea mays), 3'ss of exon 2
--------------------------------------------------------------------------------tttcacc----ttctttaaaccagcattaggaagttt--tgctatccattgttcaattaatagtac-ttatgttcttataa-----atctcatttgctggattatataccagGCATCTACAGCGACCACAGACACTAGCTGCGAGTCTGTGGTCATGAGCGGTCAGCACCAACAACAGCAAAACCCAACACCTCAGCATCCTCAAAGGGATG
||| | | | ||| | | || | | | || || | || || | | | | |||| || || | || |||||||| | || | | || | ||| ||| ||||| ||||| ||||| ||||||||||| | || ||||||||| | ||||||||||||||| || || |||||||| | |
gtgagctacttttctcttttcaaatgtacatgggcttgaactagaaaatggattggtttcatgatgcatggcttgctgcattttaacaaagtctgttacagtattgtttacatgcctactgtaattctttttttccctgcttatgcattatctttttctgcttgctataacatttgcttgtaaatttgc-agCCTTCTGTAGCCACCACCGACACAAGCTGTGAGTCTGTGGTGACAAGTGGTCAGCACAACCAACAGCAAAACCCAGCAGTTCTGCATCCTCCACAAAGGG
upper sequence: Vv10s0003g04670.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GRMZM2G003509_T02 (Zea mays), 3'ss of exon 2
-------------------------------------------------------------tttcaccttctt-taaaccagcattaggaagttttgctatccattgttca---attaatagtacttatgttcttataaatctcatttgctggattatataccagGCATCTACAGCGACCACAGACACTAGCTGCGAGTCTGTGGTCATGAGCGGTCAGCACCAACAACAGCAAAACCCAACACCTCAGCATCCTCAAAGGGATG
| | || | || | || | || | | || | | | || | | |||| || ||| | || | || |||||||| | | ||| | ||| ||| ||||| ||||| ||||||||||||||||| | || ||||||||| | || |||||||||||| || || |||||||| | |
gtgagcaccttctcccttttcgactgtaccggctgcattaattttttttcttgacacagtctgtaacagtattgttcacatgtcctactatggttgtttcttccctgcttatgcattactatatcttgttttacttgctataacatttgctctgtaaatctgcagCCTTCTGTAGCCACCACCGACACAAGCTGCGAGTCTGTGGTGACAAGTGGTCAGCACAAGCAGCAGCAAAACCCAGCAGTTCTGCATCCTCCACAAAGGG
upper sequence: Vv10s0003g04670.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA15G13640.1 (Glycine max), 3'ss of exon 2
-----------tttcaccttctttaaaccagcattaggaagttttgctatccattgttcaattaatagtacttatgttcttataaatctcattt--gctggattatataccagGCATCTACAG---CGACCACAGACACTAGCTGCGAGTCTGTGGTCATGAGCGGTCAGCACCAACAACAGCAAAACCCAACACCTCAGCATCCTCAAAGGGATG
| || | ||| | | | | ||||| | || || ||| | | ||| | || | ||| | | || | | ||||| ||| | | | |||||||||| |||||| ||||||||||| ||||| ||||| ||||||| |||||||||||||||||||||||| | ||||||
gtgatattctctatctctctctctgt-ctttcttctcttcattttgtgaatgctttttgtattttctgaatatattaatggctgaaccatgttttggtttgaactttgaacagGCTTCTGCTGGTACTACCACAGACAATAGCTGTGAGTCTGTGGTAATGAGTGGTCAAAACCAACA---GCAAAACCCAACACCTCAGCATCCCAACCGGGATG
upper sequence: Vv10s0003g04670.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA09G02750.1 (Glycine max), 3'ss of exon 2
tttcaccttctttaaaccagcattaggaagttttgctatccattgttcaattaatagtacttatgttcttataaatctcatttgctggattatataccagGCATCTACAG---CGACCACAGACACTAGCTGCGAGTCTGTGGTCATGAGCGGTCAGCACCAACAACAGCAAAACCCAACACCTCAGCATCCTCAAAGGGATG
| |||| || || ||| || | | || || ||| ||| || | || || | | || || | | | || |||| ||| ||| | |||||||||| |||||| ||||||||||| ||||| ||||| ||||||| |||||||||||||||||||||||| | |||||||
gtgagcctttcttctctttattttgtgaatgctttttgtgttttttttaat--ataataatgattcaaccatg--ttttggtt--tgaactttgaac-agGCTTCTGCAGGTACTACCACAGACAATAGCTGTGAGTCTGTGGTTATGAGTGGTCAAAACCAACA---GCAAAACCCAACACCTCAGCATCCCAATAGGGATG
upper sequence: Vv10s0003g04670.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: AT1G30490.1 (Arabidopsis thaliana), 3'ss of exon 2
-----------------tttcac------cttctttaaaccagcat-taggaagttttgctatccattgttcaattaatagtacttatgttcttataaat---ctcat----ttgctggattatataccagGCATCTACAGCGACCACAGACACTAGCTGCGAGTCTGTGGTCATGAGCGGTCAGCACCAACAACAGCAAAACCCAACACCTCAGCATCCTCAAAGGGATG
||| | | | || | || | || | || ||| ||| | |||| ||| || |||| ||| | | || | | ||| || | | |||| ||| |||||||||||| ||||| |||||||||||| |||| |||||||| | || |||||||||||||||| |||||||||||| | ||||
gtaagtccttgaatcccttttgctaaatgcattgttgagttgttatctttgatgcttgtatatgtatttgttctttaagagttctc-tgttgttagagagtgactggtgaaatctctgtgttgtgtcttagGCTTCTGGGACGACCACAGACAACAGCTGTGAGTCTGTGGTCGTGAGTGGTCAGCAACGTCAGCAGCAAAACCCAACACATCAGCATCCTCAGCGTGATG
upper sequence: Vv10s0003g04670.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: AT2G34710.1 (Arabidopsis thaliana), 3'ss of exon 2
tttcaccttctttaaaccagcattaggaagttttgctatccattgttcaatta-atagtacttatgttcttataaatctcatttgctggattatataccagGCATCTACAGCGACCACAGACACTAGCTGCGAGTCTGTGGTCATGAGCGGTCAGCACCAACAACAGCAAAACCCAACACCTCAGCATCCTCAAAGGGATG
| | || || | ||| | || | |||||| || | | | | | | | | | || | | | || |||| ||| |||||||||||| ||||| |||||||||||| |||| |||||||| || |||||||||||||||| |||||||||| ||| | ||||
---------gtaaagttcacttttcactattttctgtctctaaaactcaattctatgaagcattttgtttgaaagttgttatcttttttttggaatgt-agGCTTCTGGGACGACCACAGACAACAGCTGTGAGTCTGTGGTCGTGAGTGGTCAGCAACATCAACAGCAAAACCCAAATCCTCAGCATCAGCAACGTGATG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttcaattaatagtacttatgttcttataaatctcatttgctggattatataccagGCATCTACAGCGACCACAGACACTAGCTGCGAGTCTGTGGTCATGAGCGGTCAGCACCAACAACAGCAAAACCCAACACCTCAGCATCCTCAAAGGGATG
aattaat putative branch site (score: 3)
ttatgttcttataaat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tttcaccttctttaaaccagcattaggaagttttgctatccattgttcaattaatagtacttatgttcttataaatctcatttgctggattatataccagGCATCTACAGCGACCACAGACACTAGCTGCGAGTCTGTGGTCATGAGCGGTCAGCACCAACAACAGCAAAACCCAACACCTCAGCATCCTCAAAGGGATG
- -caccttc
- - - - - - -aaaccag
- - - - - - - - - - - - - - - - - -ctatcca