Sequence
atgc intronic sequence ATGC exonic sequencegtgtgcctgagtatttattatcttgggattttgtttataaagatatgattgttctctgtgacctgttatttttgaattatttatttaacatttctttatatgtcaaagcaataaataatctattattattccctacataaatataatattttctcaagatcatcctattttaaatatttttccatcttatacacagGTTGATGAAGAAGATTTCAATGAGGAGCAAAACTCTGTTGCTCGCCTCATACACATGTTTCATAATGATGAATCAGAGGAAATGTTTAAG
Basic information
species | Glycine max |
transcript | GLYMA14G40270.1 |
intron # | 13 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA14G40270.1 (Glycine max), 3'ss of exon 13
lower sequence: GRMZM5G825524_T02 (Zea mays), 3'ss of exon 13
gtgtgcctgagtatttattatcttgggattttgtttataaagatatgattgttctctgtgacctgttatttttgaattatttatttaacatttcttta-tatgtcaaagcaataaataatctattattattccctacataaatataatattttctcaagatcatcctattttaaatatttttccatcttatacacagGTTGATGAAGAAGATTTCAATGAGGAGCAAAACTCTGTTGCTCGCCTCATACACATGTTTCATAATGATGAATCAGAGGAAATGTTTAAG
||| | || | | | ||| || || ||||| ||| ||| || | | | || ||| | || ||| ||| | || | | | | ||| || || | ||| ||||| ||| | || | ||||| || | | || |||||||||||||||| || ||||| || |||||||| || || ||||| |||||||| || |||||||| | || || ||||| |||
--gtgagttcatacacttcgttagaaaagcgaattttta----cttgtttgttgtcttcattctgccgctt----agtgctc--ccaatattgttcagctagatcagcacaacacat--ttcaatttcattttct-------catgaagtttgctcaa------cctgtaacaa-tgtttttttattattt---tagCTTGATGAAGAAGATTTTAAGGAGGAACAGAACTCTGTAGCACGTCTCATTCACATGTTGCACAATGATGAGCCTGAAGAGATGTTGAAG
upper sequence: GLYMA14G40270.1 (Glycine max), 3'ss of exon 13
lower sequence: GRMZM5G844195_T02 (Zea mays), 3'ss of exon 14
gtgtgcctgagtatttattatcttgggattttgtttataaagatatgattgttctctgtgacctgttatttttgaattatttatttaacatttctttatat-gtcaaagcaataaataatctattattattccctacataaatataatattttctcaagatcatcctattttaaatatttttccatcttatacac-agGTTGATGAAGAAGATTTCAATGAGGAGCAAAACTCTGTTGCTCGCCTCATACACATGTTTCATAATGATGAATCAGAGGAAATGTTTAAG
| ||| | | |||||| | |||| | ||| | || ||| ||| | || | ||| || | || | | | | || || | || ||| ||||| | | | | | | | ||| | | | || || | | ||| | || || ||||||||||||| || || ||||| ||||||||||| || || ||||| |||||| | || |||||||| | || || ||| | |||
--------------gtgagatcatac-actttgtt-agaaaggtgaaattttact-tgtttgttgtcttcgttctgatgcttagttctcccaatattgttcagctagatcagtaca-aacacatttcaattccatt------ttcattttctcatgaagtttgctcaacttgtaacaatgttcttttaattattttagCTTGATGAAGAAGACTTTAAGGAGGAACAAAACTCTGTAGCGCGTCTCATTCACATGCTGCACAATGATGATCCTGAAGAGATGCTGAAG
upper sequence: GLYMA14G40270.1 (Glycine max), 3'ss of exon 13
lower sequence: Vv18s0001g14680.t01 (Vitis vinifera), 3'ss of exon 13
gtgtgcctgagtatttattatcttgggattttgtttataaagatatgattgttctctgtgacctgttatttttgaattatttatttaacatttctttatatgtcaaagcaataaataatctattattattccctacataaatataatattttctcaagatcatcctattttaaatatttttccatcttatacacagGTTGATGAAGAAGATTTCAATGAGGAGCAAAACTCTGTTGCTCGCCTCATACACATGTTTCATAATGATGAATCAGAGGAAATGTTTAAG
||| | || ||| | | | | | | ||| | | | | || | |||| | | | | | | || | ||| | ||| || | | | || ||||||| || |||||||| || || ||||| ||||| ||||| |||||||||||||| | |||||||| | || |||||||| |||
-----------------------------------------------------------------------------------ttttattttattttttccttttactttcttcttgaattatcactgtagattg-gtatagataacaatcttt---gtttttcttgttt-----acttt---atgcaaca-atagCTTGATGAGGAGGATTTCAAGGATGAACAAAATTCTGTCGCTCGTCTCATACACATGTTCTACAATGATGACCCCGAAGAAATGTTGAAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tataatattttctcaagatcatcctattttaaatatttttccatcttatacacagGTTGATGAAGAAGATTTCAATGAGGAGCAAAACTCTGTTGCTCGCCTCATACACATGTTTCATAATGATGAATCAGAGGAAATGTTTAAG
tatttttccatctt CT-rich tract
tattttaaatattttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtgtgcctgagtatttattatcttgggattttgtttataaagatatgattgttctctgtgacctgttatttttgaattatttatttaacatttctttatatgtcaaagcaataaataatctattattattccctacataaatataatattttctcaagatcatcctattttaaatatttttccatcttatacacagGTTGATGAAGAAGATTTCAATGAGGAGCAAAACTCTGTTGCTCGCCTCATACACATGTTTCATAATGATGAATCAGAGGAAATGTTTAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA