Sequence
atgc intronic sequence ATGC exonic sequence...atttaattattgtcccagtattctctcttttagatacttctcctgtccctttctttcattatattcttttgacatttttatcttgacgtggaatgttaagGTGGATTTGGAACATAATCATTATCGGTCTTTCCAAGGTTTGACTTGCTTGATGCAAATCTCAACCAGGACTGAAGATTTTGTTATAGATACTCTGAAGG
Basic information
species | Glycine max |
transcript | GLYMA19G29260.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA19G29260.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G118917_T02 (Zea mays), 3'ss of exon 2
--atttaattattgtcccagtattctctctt--ttagatacttctcctgtccctttctttcattatattcttttgacatttttatcttgacgtggaatgttaagGTGGATTTGGAACATAATCATTATCGGTCTTTCCAAGGTTTGACTTGCTTGATGCAAATCTCAACCAGGACTGAAGATTTTGTTATAGATACTCTGAAGG
|| | ||| | | | | | |||| ||| || || | || | | | |||| | || ||||| | | | | | || |||| ||||||||||| || |||||| |||| || || |||||||| ||||||||||| || ||||| || || || || ||| || | || ||||| |||
atatgcatctatgcactgaacactgtttcttaattaaattattttgatgcactgagcactgtttat-taattaaactattttgacccttccatcat---ttcagGTCGATTTGGAACACAACCATTATAGGTCGTTTCAGGGTTTGACATGCTTGATGCAGATTTCAACAAGAACAGAGGACTTTATTGTTGACACTCTTAAGC
upper sequence: GLYMA19G29260.1 (Glycine max), 3'ss of exon 2
lower sequence: AT5G35910.1 (Arabidopsis thaliana), 3'ss of exon 2
----atttaattat-tgtcccagtattctctcttttagatacttctcctgtccctttctttcattatattcttttgacatttttatcttgacgtggaatgttaagGTGGATTTGGAACATAATCATTATCGGTCTTTCCAAGGTTTGACTTGCTTGATGCAAATCTCAACCAGGACTGAAGATTTTGTTATAGATACTCTGAAGG
|| |||| | ||| | | | || || | | | ||| || | |||| || | ||||| | || | | || |||| ||| |||| |||||||| ||| | ||||| ||||| ||||| |||||||||||||| || ||||| || || |||| | | | ||||| | |||
ctctccttgattagataagccaaaaaaatatattcaagtttgagttgccaatgcttatttctcccct-ttctcttaagttttttgtttttgctc----tttttagGTTGATCTGGAGCATAATCAGTATAGATCTTTTCAAGGATTGACATGCTTGATGCAAATTTCCACCAGAACAGAGGATTATATAGTTGATACATTTAAGC
upper sequence: GLYMA19G29260.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv08s0056g01320.t01 (Vitis vinifera), 3'ss of exon 1
atttaattattgtcccagtattctctcttttagatacttctcctgtccctttctttc-attatattcttttgacatttttatcttgacgtggaat-gttaagGTGGATTTGGAACATAATCATTATCGGTCTTTCCAAGGTTTGACTTGCTTGATGCAAATCTCAACCAGGACTGAAGATTTTGTTATAGATACTCTGAAGG
|| || | || | | | | | ||| | | | | | | || | |||| | | | | |||| | || || |||| ||| ||||||||||||| ||||| ||||| ||||| ||||||||||||||||||||||| || |||||||| ||||||||| | ||||| || |||
--ctatcacttctaacaagaaatttacgtgcaaataatatgtacataatgtcatctggactagctaattttcaggtctctttctttttgaactattgtctagGTTGATCTGGAACATAATCAGTATCGATCTTTTCAAGGGTTGACTTGCTTGATGCAAATCTCTACTAGGACTGAGGATTTTGTTGTTGATACACTAAAGC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tccctttctttcattatattcttttgacatttttatcttgacgtggaatgttaagGTGGATTTGGAACATAATCATTATCGGTCTTTCCAAGGTTTGACTTGCTTGATGCAAATCTCAACCAGGACTGAAGATTTTGTTATAGATACTCTGAAGG
tcttgac putative branch site (score: 3)
tttcattatattcttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
atttaattattgtcccagtattctctcttttagatacttctcctgtccctttctttcattatattcttttgacatttttatcttgacgtggaatgttaagGTGGATTTGGAACATAATCATTATCGGTCTTTCCAAGGTTTGACTTGCTTGATGCAAATCTCAACCAGGACTGAAGATTTTGTTATAGATACTCTGAAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
- - - - - tgtccca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgacgtg