Sequence
atgc intronic sequence ATGC exonic sequencegtaagtttcacaatatgcttaaggggggccataatattttccatgacgttaatctacatagtttccaaatgggttttttactttctaacttgtatgtatgtgcagGAGGATGGATGGGTGGTGTGCAGGGTTTTCAAGAAGAAGAACCTATTCAAGCTTGGAACCGAAGGCGGAGGAAGCAGCAGCGCCAGCATGGCCGGCTTAG
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: Vv18s0089g01120.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: 13113.m00212 (Oryza sativa), 3'ss of exon 2
gtaagtttcacaatatgcttaaggggggccataatattttccatgacgttaatctacatagtttccaaatgggttttttactttctaac---ttgtatgtatgt-gcagGAGGATGGATGGGTGGTGTGCAGGGTTTTCAAGAAGAAGAACCTATTCAAGCTTGGAACCGAAGGCGGAGGAAGCAGCAGCGCCAGCATGGCCGGCTTAG--
||| | | | | | | | | ||| | || | | ||| || | || | | | | ||||||||| |||||||||||||||||||| |||||||||||| | | |||||| | || || ||||| || | |||| | | ||| | |
---------ttgatagtttagaatattttcccttctcctcctctcgcatcgatcgattgcattagggtttcgaactttcacctactgatcgatcgccgactcgccgcagGAGGACGGATGGGTGGTGTGCAGGGTGTTCAAGAAGAAGTGCTTCTTCAAGATCGGCGGCGGCGGCGGCGGCGAGGGGAGCGGGGGGA--GCCAGGGAGGGG
upper sequence: Vv18s0089g01120.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GRMZM2G435824_T01 (Zea mays), 3'ss of exon 2
------------------------------------------------------------------------gtaagttt-cacaatatgcttaaggggggccataatattttccatgacgttaatct---acatagtttccaaatgggttttt-----tactttctaacttgtatgtatgtgcagGAGGATGGATGGGTGGTGTGCAGGGTTTTCAAGAAGAAGAACCTATTCAAGCTTGGAACCGAAGGCGGAGGAAGCAGCAGCGCCAGCATGGCCGGCTTAG---
| |||| || | | || | | | | | || | | | | | | | | |||| | | | || | ||| | || |||||||||||| ||||||||||||||| | || |||||||||||| | | |||||| |||| || ||||| ||| |||| || | |||| || || |
gtgcgttgttaattaccttctcgcgctccgatcctagctctctccactaaccactatatatcgatccgcgccgcgtgtttgcatgcgaaatctgagcgcgccattcacatctccgttaattcttgtgttaggttttttttctgtgttgaatgttgatcatgcttgtcgatactgtcgtctgtgcagGAGGACGGATGGGTGGTGTGCCGCGTGTTCAAGAAGAAGTGCTTCTTCAAGATTGG---CGGAGGCGAAGGGAGCACCACCAGCAGCCAGGGCGCGGATGCCG
upper sequence: Vv18s0089g01120.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GRMZM2G099144_T01 (Zea mays), 3'ss of exon 2
-----------------------------------------------------------gtaagt-ttcacaatatgcttaagggg---ggccataatattttccatgacgttaatctacata--gtttccaaatgggttttttactttctaacttgtat-----gtatgtgcagGAGGATGGATGGGTGGTGTGCAGGGTTTTCAAGAAGAAGAACCTATTCAAGCTTGGAACCGAAGGCGGAGGAAGCAGCAGCGCCAGCATGGCCGGCTTAG---
||| | | ||| ||| | || | | | | || | | ||| || ||||| || | | | | | | ||| || ||| |||||||| ||||||||||||||| | || |||||||||||| | | |||||| |||| || |||| ||| |||| |||| ||| || || |
gtacgttgattaccttcttgctctccgatgctctctccactatatatatgtacccggccgtatgcatgtttaatttgcatgagaaatctgagcgaattgttgcctgcatctcagttcttgttagggtttctgtgtgtgctgatcatgcatgcatgtctattaactgtctgttcagGAGGACGGATGGGTGGTGTGCCGCGTGTTCAAGAAGAAGTGCTTCTTCAAGATTGG---CGGGGGCGAAGGGAGCACCAGCCAGAGCGCGGACGCTGGCGGCC
upper sequence: Vv18s0089g01120.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA09G36820.1 (Glycine max), 3'ss of exon 2
--------gtaagtttcacaatatgcttaaggggggccataatattttccatgacgttaatctacatagtttccaaatgggttttttactttctaacttgtatgtatgtgcagGAGGATGGATGGGTGGTGTGCAGGGTTTTCAAGAAGAAGAACCTATTCAAGCTTGGAACCGAAGGCGGAGGAAGCAGCAGCGCCAGCATGGCCGGCTTAG--
| |||| || || || | ||| || ||| || | || || ||| || | |||||| || | ||| || || |||||| || |||| ||||| |||||||||||||| || |||||||||||||| |||||||| ||| || ||||| || | | |||| || || | |
gatttgatttttgttttgaaagatact-aggggtggatatagaatca--cgtggtgtcaattaac------tacaaatg---cttatgatttata-tatgaatgtatttgtagGAAGATGGCTGGGTGGTGTGCAGAGTGTTCAAGAAGAAGAATTTATTCAAGATTGAAAATGAAGGTGGGTCTACACATAA-ACCAG-ATCACCAAATCAACA
upper sequence: Vv18s0089g01120.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA12G00540.1 (Glycine max), 3'ss of exon 2
gtaagtttcacaatatgcttaaggggggccataatattttccatgacgttaatctacatagttt---ccaaatgggttttttactttctaacttgtatgtatgtgcagGAGGATGGATGGGTGGTGTGCAGGGTTTTCAAGAAGAAGAACCTATTCAAGCTTGGAACCGAAGGCGGAGGAAGCAGCAGCGCCAGCATGGCCGGCTTAG--
|| || || || | | | || | || | ||||| || | || | | | | | || || | || |||||| || |||| ||||| |||||||||||||| || |||||||||||||| | |||||| ||| || ||||| || | | |||| || | | |
-----cttttggatttgatttttgttttcaaagctactaggggtg--gataatc-acgtggtgtaaactacgtaaatgcttatgatttatatatgaatgtatttgtagGAAGATGGCTGGGTGGTGTGCAGAGTGTTCAAGAAGAAGAATTTGTTCAAGATTGTAAATGAAGGTGGGTCTACACATAAT-CCAG-ATCAACAAATCAACA
upper sequence: Vv18s0089g01120.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: EFJ22020 (Selaginella moellendorffii), 3'ss of exon 2
gtaagtttcacaatatgcttaaggggggccataatattttccatgacgttaatctacatagtttccaaatgggttttttactttctaacttgtatgtatg---tgcagGAGGATGGATGGGTGGTGTGCAGGGTTTTCAAGAAGAAGAACCTATTCAAGCTTGGAACCGAAGGCGGAGGAAGCAGCAGCGCCAGCAT-GGCCGGCTTAG
||| || || | | | | | || || | ||| ||| | || | | || ||||||| ||||| |||||||| ||| |||||||||||||| ||| || | || | | |||| || || | ||| | || | |
------------------------------gtaagatcctc--tcgtacttggcagcttttttcttctataaccctcttatttttttggttttggctctgaaatgcagGATGATGGCTGGGTGGTTTGCCGGGTTTTCAAGAAGCGCAACAACAGCATCAAGGTGCTTGATCGGGATATAAGCTGCGGCTACGACATCGACCAGATCG- atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aatctacatagtttccaaatgggttttttactttctaacttgtatgtatgtgcagGAGGATGGATGGGTGGTGTGCAGGGTTTTCAAGAAGAAGAACCTATTCAAGCTTGGAACCGAAGGCGGAGGAAGCAGCAGCGCCAGCATGGCCGGCTTAG
ttctaac putative branch site (score: 1)
ttttttactttctaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaagtttcacaatatgcttaaggggggccataatattttccatgacgttaatctacatagtttccaaatgggttttttactttctaacttgtatgtatgtgcagGAGGATGGATGGGTGGTGTGCAGGGTTTTCAAGAAGAAGAACCTATTCAAGCTTGGAACCGAAGGCGGAGGAAGCAGCAGCGCCAGCATGGCCGGCTTAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA