Sequence
atgc intronic sequence ATGC exonic sequence...tcatattgaataaacatgattggaacctagttgttcacttgtattggtatgtgcaaatcctgtctttatggttttgtctgatttcttggtcttcggatagGATGTAGAAGGTATGATGTCTATCTCTGATGAGGCAGCAGAGGCTCGGGATTCTTTGAGCGATGACAAAGAAATTGTCAACACTTACGAG
Basic information
species | Glycine max |
transcript | GLYMA03G03120.2 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA03G03120.1 (Glycine max), 3'ss of exon 5
lower sequence: AT1G71820.1 (Arabidopsis thaliana), 3'ss of exon 5
------------------------------------------------------------------tcatattgaat--aaacatgattggaacctagttgttcacttgtattggtatgtgcaaatcctgtctttatggttttgtctg-atttcttggtcttcggata-gGATGTAGAAGGTATGATGTCTATCTCTGATGAGGCAGCAGAGGCTCGGGATTCTTTGAGCGATGACAAAGAAATTGTCAACACTTACGAG
| | ||||| ||| || | | | | || || || || ||| | || ||| | || | | | || | |||| | ||||||||||||||||||||| || |||| ||| || || | |||| ||||||||||||| ||||| |||||||| || |||||||| |||
gtagatatgccgatgagcactgattgtattgcttacagtatttggttcagtgttgtccttctaacttattcttgaacgcaaatatatatagctctgcatggtcgtctcagatgtttaaatgctttccaagtttttgtcaacttatttttacctcattctcttttttcaagGATGTAGAAGGTATGATGTCAATTTCTGTTGAAGCTGCTGCGGCTAGGGATTCTTTGAGTGATGATAAAGAAATCGTTAACACTTATGAG
upper sequence: GLYMA03G03120.1 (Glycine max), 3'ss of exon 5
lower sequence: Vv12s0034g02360.t01 (Vitis vinifera), 3'ss of exon 4
---tcatattgaataaacatgattggaacctagttgttcacttgtattggtatgtgcaaatcctgtctttatggttttgtctgatttcttggtcttcggatagGATGTAGAAGGTATGATGTCTATCTCTGATGAGGCAGCAGAGGCTCGGGATTCTTTGAGCGATGACAAAGAAATTGTCAACACTTACGAG
|| ||| || | | | || | || | ||| | |||| | | | | | | | | | | | | || || | |||| | ||||||| ||||| |||||||| || |||| ||| ||| | |||||||||||||||||||| ||||| |||||| | ||||||| ||||||
ttatcctatcaaaaagaaaaacttagcacttttttgacc--ttgttatcttctattaatgttgtatggtgaccatctagttatgttcttaaatctttt-acagGATGTGGAAGGGATGATGTCAATTTCTGTTGAAGCATCTGAGGCTCGGGATTCTTTGAGTGATGATAAAGAACTCATCAACACGTACGAG
upper sequence: GLYMA03G03120.1 (Glycine max), 3'ss of exon 5
lower sequence: Vv03s0097g00670.t01 (Vitis vinifera), 3'ss of exon 4
--tcatattgaataaacatgattggaacctagttgttcacttgtattggtatgtgcaaatcctgtctttatggttttgt--ctgatttcttggtcttcggatagGATGTAGAAGGTATGATGTCTATCTCTGATGAGGCAGCAGAGGCTCGGGATTCTTTGAGCGATGACAAAGAAATTGTCAACACTTACGAG
|| || ||| | ||| | | | || || || | | | | ||| ||| | | || | | | | ||||| |||| | |||| || ||||| |||||||| || |||| ||| ||| | |||||||||||||||||||| ||||| |||||| | ||||||| || |||
caccactttttatagccctgaaacttatc-actttttgacct-cgctatcttctattaatgctg-catagtgactatctagttatcttcttaatctttt-acagGACGTGGAAGGCATGATGTCAATTTCTGTTGAAGCATCCGAGGCTCGGGATTCTTTGAGTGATGATAAAGAACTCATCAACACGTATGAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ggtatgtgcaaatcctgtctttatggttttgtctgatttcttggtcttcggatagGATGTAGAAGGTATGATGTCTATCTCTGATGAGGCAGCAGAGGCTCGGGATTCTTTGAGCGATGACAAAGAAATTGTCAACACTTACGAG
gtctgat putative branch site (score: 4)
tcttc putative PPT
tctttat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tcatattgaataaacatgattggaacctagttgttcacttgtattggtatgtgcaaatcctgtctttatggttttgtctgatttcttggtcttcggatagGATGTAGAAGGTATGATGTCTATCTCTGATGAGGCAGCAGAGGCTCGGGATTCTTTGAGCGATGACAAAGAAATTGTCAACACTTACGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA
- - - - - - - catgatt
- - - - - - - - - - - - - - - - - -cacttgt
- - - - - - - - - - - - - - - - - - - - - - - -tatgtgc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ggttttg