Sequence
atgc intronic sequence ATGC exonic sequence...ccgaatagagtccatgtattttgcttctcttctgttattttcaaaagatctaactctagtatgaaattgtaatttctttatcttgtttcatgtcttacagGTCAGATGTTCTTGGTCAGTTCATGCCTTTGGTTGGTATTGACTGGTCACAGACAGGTGTTGCACATTTATTCTCCGCTATCAAG
Basic information
species | Glycine max |
transcript | GLYMA04G04060.1 |
intron # | 9 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA04G04060.1 (Glycine max), 3'ss of exon 9
lower sequence: LOC_Os11g40080.1 (Oryza sativa), 3'ss of exon 3
--ccgaatagagtccatgtattttgcttctcttctgttattttcaaaagatctaactctagtatgaaattgtaatttctttatcttgtttcatgtct-tacagGTCAGATGTTCTTGGTCAGTTCATGCCTTTGGTTGGTATTGACTGGTCACAGACAGGTGTTGCACATTTATTCTCCGCTATCAAG
| ||| | || | | | ||| | | | ||||| | | | || | | | || | | | || | || | | ||||| ||||||||||| ||||||||||| |||||||| |||| ||||| || | ||||||||||||||||| || || || |||
aactgaaacaattcataggaactagctgagttcacaaaacatgcaaaaagt---attttaacttaacctaacaagtgcctacaatttatcaatataaatgtagGTCTGATGTTCTTGGCCAGTTCATGCCGCTGGTTGGTGTTGATTGGTCTCAAAATGGTGTTGCACATTTATTTTCTGCAATAAAG
upper sequence: GLYMA04G04060.1 (Glycine max), 3'ss of exon 9
lower sequence: AT5G42870.2 (Arabidopsis thaliana), 3'ss of exon 4
-ccgaatagagtccatgtattttgcttctcttctgttattttcaaa---agatctaactctagtatgaaattgtaatttct-----ttatcttgtttcatgtc--------ttacagGTCAGATGTTCTTGGTCAGTTCATGCCTTTGGTTGGTATTGACTGGTCACAGACAGGTGTTGCACATTTATTCTCCGCTATCAAG
| | | ||| | ||| | | | | |||| || || | || || | || | || | |||| ||| ||| || || | | || || ||||| | || ||||| ||||||||||||||||| || |||||||| ||||||||| ||||||| || || ||| | |||
gtaaagaaaaacacatttggttttatattatgtttttatattttaagccaagtccaaaacctgtttctgtttctgattttccttacttactttgctttatattattgtttgtcgtagATCGGATGTATTAGGCCAGTTTATGCCTTTGGTTGGTATAGATTGGTCACAAACAGGTGTTACACATTTGTTTTCGGCTGTAAAG
upper sequence: GLYMA04G04060.1 (Glycine max), 3'ss of exon 9
lower sequence: Vv18s0001g10680.t01 (Vitis vinifera), 3'ss of exon 6
------------------------------------------------------------ccgaatagagtc---catgtattttgcttctcttc-tgttattttcaaaagatc-ta-actctagtatgaaattgt---aatttctttatcttgtttcatgtcttacagGTCAGATGTTCTTGGTCAGTTCATGCCTTTGGTTGGTATTGACTGGTCACAGACAGGTGTTGCACATTTATTCTCCGCTATCAAG
| || || | | | |||| | || || | | || ||||| || | ||| | || | | | | ||| ||||| | | | |||||||||||||||||| || |||||||||||| ||||||| | || ||||||||||||||||| |||||| |||| || ||||| |||
gtaagggtactcaaatctttttctaaggttaaaaattgataccttgtatgttagatgtttttggattgaatttcacttctattatagtttggttgatacaagcaccagtagatcatatattcttgcttggacccatctgactccttttgtcttgcattct-tattacagGTCAGATGTTCTAGGGCAGTTCATGCCTATGGTTGGAGTAGATTGGTCACAGACAGGTGTAGCACATCTATTTTCTGCTATTAAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.agatctaactctagtatgaaattgtaatttctttatcttgtttcatgtcttacagGTCAGATGTTCTTGGTCAGTTCATGCCTTTGGTTGGTATTGACTGGTCACAGACAGGTGTTGCACATTTATTCTCCGCTATCAAG
atctaac putative branch site (score: 2)
tatgaaattgtaattt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ccgaatagagtccatgtattttgcttctcttctgttattttcaaaagatctaactctagtatgaaattgtaatttctttatcttgtttcatgtcttacagGTCAGATGTTCTTGGTCAGTTCATGCCTTTGGTTGGTATTGACTGGTCACAGACAGGTGTTGCACATTTATTCTCCGCTATCAAG
- - - - - -ccatgta
- - - - - - - - - - - gcttctc
- - - - - - - - - - - - - - -ttctgtt