Sequence
atgc intronic sequence ATGC exonic sequence...taatgtgcagtcatatttattatctgcttattcttgccatgtgtaaaatttgcaatttgtcttcttttggtatataacatattgagaactacccttgcagTGCATGACTGCCAATTGGTGGACGATATTCCTGTTGAAAAGCTGTTAATCCATGACGTACCAGTGGATATCATTTGTACTCCAACACAGGTCATTTTCAC
Basic information
species | Glycine max |
transcript | GLYMA02G08860.1 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA02G08860.1 (Glycine max), 3'ss of exon 5
lower sequence: LOC_Os12g07020.1 (Oryza sativa), 3'ss of exon 4
--------------------------taatgtgcagtcatatttattatctgcttattctt-gccatgtgtaaaat--ttgcaatttgtcttcttt------tggtatataac------atattgagaact------acccttgcagTGCATGACTGCCAATTGGTGGACGATATTCCTGTTGAAAAGCTGTTAATCCATGACGTACCAGTGGATATCATTTGTACTCCAACACAGGTCATTTTCAC
| | | || | || | | |||| || || | |||| | |||| ||| || ||| || | ||||| | |||| |||| | ||||||||||||| ||||| ||| | || ||||| ||||| ||||||||| | ||||| |||||||| || || || || |||||||| |||||||| |||||
gtgagtttttttatattgattcagctggttatcccttcttggataacctttatatattttttatcaaatttaaattaattgccttttagctcatttgttccttgattaataactaatgtaaattgccaactgtgtctatgactgcagTGCATGACAAACAATTAGTGAATGACATTCCAGTTGAGAAGCTGTTAGTTCATGATGTACCAGTTGACATTATCTGCACTCCAACTCAGGTCATATTCAC
upper sequence: GLYMA02G08860.1 (Glycine max), 3'ss of exon 5
lower sequence: Vv18s0072g00300.t01 (Vitis vinifera), 3'ss of exon 4
taatgtgcagtcatatttattatctgcttattcttgccatgtgtaaaatttgcaatttgtcttcttttggtatataacatattgagaa-ctacccttgcagTGCATGACTGCCAATTGGTGGACGATATTCCTGTTGAAAAGCTGTTAATCCATGACGTACCAGTGGATATCATTTGTACTCCAACACAGGTCATTTTCAC
|| || | ||| | || | ||| || || ||| ||| | | || | | || |||| || ||||||| ||||| |||||||| || |||||||||||||| |||||||||||||||||||| ||||| ||||| || || || ||||| || |||||||| ||
-tatatgtggccatctgatttgttatcttcccctccccccaccccctctttttctttttttctaattatcgcttcattattttgattctctgattttgcagTACATGATGAGCAATTGGTCGATGATATTCCTGTTGAGAAGCTGTTAATCCATGACGTGCCAGTTGATATTATATGCACCCCAACCCAAGTCATTTTTAC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aaatttgcaatttgtcttcttttggtatataacatattgagaactacccttgcagTGCATGACTGCCAATTGGTGGACGATATTCCTGTTGAAAAGCTGTTAATCCATGACGTACCAGTGGATATCATTTGTACTCCAACACAGGTCATTTTCAC
atataac putative branch site (score: 3)
ctaccctt putative PPT
tatataacatattga 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
taatgtgcagtcatatttattatctgcttattcttgccatgtgtaaaatttgcaatttgtcttcttttggtatataacatattgagaactacccttgcagTGCATGACTGCCAATTGGTGGACGATATTCCTGTTGAAAAGCTGTTAATCCATGACGTACCAGTGGATATCATTTGTACTCCAACACAGGTCATTTTCAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGTGGA
- - -tgcagtc
- - - - - - - - - - - tctgctt
- - - - - - - - - - - - - - - - cttgcca
- - - - - - - - - - - - - - - - - - - - - - - - tttgcaa