Sequence
atgc intronic sequence ATGC exonic sequencegtaatttcctttctttctacttgtctctcccttattatttgatttttattctaagccatgccttaatgtcctttccacagCTTGCCCTGCTTATTATTTGGGGTTTGCCTGAGGGATACCTTTATTCCAGAAGGTCGGAAGCTTAGAGATCCCAGAAGACTATTTGCACCTGGCCGCATG
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: Vv14s0006g01030.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA18G04540.1 (Glycine max), 3'ss of exon 2
----------------------------------------------------------------------------gtaatttcctttctttctacttgtctctcccttattatttgatttttat-----tctaagccatgccttaatgtcctttccacagCTTGCCCTGCTTATTATTTGGGGTTTGCCTGAGGGATACCTTTATTCCAGAAGGTCGGAAGCTTAGAGATCCCAGAAGACTATTTGCACCTGGCCGCATG-
| ||| | || || | | | | || || || | || ||| ||| ||||| ||| ||| |||||||||||||||| || || |||||||||||| || ||||| || || || ||| | |||||||||||||| || ||||| | ||||||||| | |||
ttggtactgccctttctgtgatatggatatggccgtattgggtttcaactttcaagtgcatgtgatttgttattgatttgtttttatgtttattattaatatggtgcatagtaaaatatcatgatgatctcttaaaccaggccttgatga--tttaaacagcTTGCCCTGCTTGTTGTTCTTGGTTTGCCTGAGAGACACCTTCATACCTGAGGGTAGAAAGCTTAGAGATCCAAGGAGACTTTATGCACCTGGAAGAATGT
upper sequence: Vv14s0006g01030.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA11G33660.1 (Glycine max), 3'ss of exon 2
------------------------------------------------------------------gtaatttcc--tttctttctacttgtctctcccttattat---------ttgatttttat--------tctaagccatgccttaatgtcctttccacagCTTGCCCTGCTTATTATTTGGGGTTTGCCTGAGGGATACCTTTATTCCAGAAGGTCGGAAGCTTAGAGATCCCAGAAGACTATTTGCACCTGGCCGCATG
|| || ||| ||| || |||| | | |||||| | | | | || ||| ||| ||||| ||| ||| ||||||||||||||||||| || |||||||||||| || ||||| || || || ||| | |||||||||||||| || || || | ||||||||| | |||
gttggtattgccctttctgtgatatggatatgggcacattgggtttcaactttgaagtgcatgtgattagttcttgatttttttttatttgttttttgtttattacggagcatagtaaaatatcatgacgatctcttaaaccaggccttgatga--tttaaacagCTTGCCCTGCTTATTGTTCTTGGTTTGCCTGAGAGACACCTTCATACCTGAGGGTAGAAAGCTTAGAGATCCAAGGAGGCTTTATGCACCTGGAAGAATG
upper sequence: Vv14s0006g01030.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA11G33660.2 (Glycine max), 3'ss of exon 2
------------------------------------------------------------------gtaatttcc--tttctttctacttgtctctcccttattat---------ttgatttttat--------tctaagccatgccttaatgtcctttccacagCTTGCCCTGCTTATTATTTGGGGTTTGCCTGAGGGATACCTTTATTCCAGAAGGTCGGAAGCTTAGAGATCCCAGAAGACTATTTGCACCTGGCCGCATG
|| || ||| ||| || |||| | | |||||| | | | | || ||| ||| ||||| ||| ||| ||||||||||||||||||| || |||||||||||| || ||||| || || || ||| | |||||||||||||| || || ||
gttggtattgccctttctgtgatatggatatgggcacattgggtttcaactttgaagtgcatgtgattagttcttgatttttttttatttgttttttgtttattacggagcatagtaaaatatcatgacgatctcttaaaccagGCCTTGATGA--TTTAAACAGCTTGCCCTGCTTATTGTTCTTGGTTTGCCTGAGAGACACCTTCATACCTGAGGGTAGAAAGCTTAGAGATCCAAGGAGGCT-------------------
upper sequence: Vv14s0006g01030.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: AT5G37710.1 (Arabidopsis thaliana), 3'ss of exon 2
gtaatttcctttctttctacttg-tctctcccttattatttgatttttattctaagccatgccttaatgtcc----tttccacagCTTGCCCTGCTTATTATTTGGGGTTTGCCTGAGGGATACCTTTATTCCAGAAGGTCGGAAGCTTAGAGATCCCAGAAGACTATTTGCACCTGGCCGCATG
|||| | | ||| | || ||| || | || || | | || || || | | | || |||||||||| ||||| || ||| ||||| ||||||||||| ||||| || ||||||||||| || |||||||| ||||| || | ||| ||||| || ||
gtaagtgtcgaacttcgaaaatgctcttgttggaatgaatttgttataggtatagttcaacattttgtattcgttgttcggacagCTTGCCGTGCTTGTTGTTTCTAGTTTGTCTGAGGGATACATTTATACCGGAAGGTCGGAAACTAAGAGATCCTAGAAGGCTTTATGCTCCTGGTCGAATT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tctcccttattatttgatttttattctaagccatgccttaatgtcctttccacagCTTGCCCTGCTTATTATTTGGGGTTTGCCTGAGGGATACCTTTATTCCAGAAGGTCGGAAGCTTAGAGATCCCAGAAGACTATTTGCACCTGGCCGCATG
ccttaat putative branch site (score: 4)
tgtcctttcc CT-rich tract
ttattatttgattttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaatttcctttctttctacttgtctctcccttattatttgatttttattctaagccatgccttaatgtcctttccacagCTTGCCCTGCTTATTATTTGGGGTTTGCCTGAGGGATACCTTTATTCCAGAAGGTCGGAAGCTTAGAGATCCCAGAAGACTATTTGCACCTGGCCGCATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATC