Sequence
atgc intronic sequence ATGC exonic sequence...gatccatttgactaatgcaaatttactttttaaatctgttatgttgataataaatttgtatgtctggctagttactcagcataagaactttatcttgcagGTTGTCTTTTTCTTGATCGTGCTTGATCGAATTATATACCTCTGCTCATTTGCACCAGGAAAAGTTATTTTCTATTTATTCAACCTTATTCTGTTCACAT
Basic information
species | Glycine max |
transcript | GLYMA19G42660.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA19G42660.1 (Glycine max), 3'ss of exon 2
lower sequence: LOC_Os01g29230.1 (Oryza sativa), 3'ss of exon 5
------------------------------gatccatttgactaatgcaaatttactttttaaatctgttatgttgataataaatttgtatgtctggctagttactcagcataagaactttatcttgcagGTTGTCTTTTTCTTGATCGTGCTTGATCGAATTATATACCTCTGCTCATTTGCACCAGGAAAAGTTATTTTCTATTTATTCAACCTTATTCTGTTCACAT
| | || || | | |||| |||| ||| | | | | |||| ||| | | ||| | ||| || | | |||| ||||| || ||||||||||||| ||| ||||||| || ||||| || || |||||||| |||||||||| ||||||||| | |||||||| | || |||||||
gtgagctccctattccattggatttgttatgtttcacttacatgctaattatttgtttttctaatatatgctatgtataagttattggaactattgg-tgattattctaccaa------ttattctgcagATTCTCTTTTTCTTGATTGTGGTTGATCGCATCATATATCTGTGGTCATTTGCCACAGGAAAAGTCATTTTCTATCTTTTCAACCTAGTGCTTTTCACAT
upper sequence: GLYMA19G42660.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G065388_T03 (Zea mays), 3'ss of exon 2
gatccatttgactaatgcaaatttactttttaaatctgttatgttgataataaatttgtatgtctggctagttactcagcataagaactttatcttgcagGTTGTCTTTTTCTTGATCGTGCTTGATCGAATTATATACCTCTGCTCATTTGCACCAGGAAAAGTTATTTTCTATTTATTCAACCTTATTCTGTTCACAT
| | | | || | | |||| ||| | || | |||| | || || | || ||| | |||||||||| ||||||||||||| ||| |||| || |||||||| || || || ||||| | || |||||| |||||||| | || |||||| | || ||||| |
----------------gtgagctaatttactgttttagttaagtt--tcatcttatgagatgttttccttattgattgcca----aacct---cttgcagGTTCTCTTTTTCTTGATAGTGGTTGACCGCATTATATATCTTTGGTCCTTTGCTACCGGCAAAGTTGTTTTCTATCTTTTTAACCTTGTGCTTTTCACGT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gataataaatttgtatgtctggctagttactcagcataagaactttatcttgcagGTTGTCTTTTTCTTGATCGTGCTTGATCGAATTATATACCTCTGCTCATTTGCACCAGGAAAAGTTATTTTCTATTTATTCAACCTTATTCTGTTCACAT
tgttgat putative branch site (score: 4)
ctttatctt putative PPT
taaatttgtat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gatccatttgactaatgcaaatttactttttaaatctgttatgttgataataaatttgtatgtctggctagttactcagcataagaactttatcttgcagGTTGTCTTTTTCTTGATCGTGCTTGATCGAATTATATACCTCTGCTCATTTGCACCAGGAAAAGTTATTTTCTATTTATTCAACCTTATTCTGTTCACAT
- -ccatttg
- - - - - - -aatgcaa
- - - - - - - - - - - - - - - - - - tgttatg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - tgtatgt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ctggcta