Sequence
atgc intronic sequence ATGC exonic sequence...caaaaggtatagtagtgaaaactgtgactagtactcttgtgttattattattattgggaatgctttgtgtgatgttaattcccttggcttgcttatgcagTATGATGTATATGGAGACCTACTAGGCCTTCTAGGGGCACATCCAGTGTCTCCACTTGTGTCACTTCACCACCTTGATGTAGTGCAACCAATATTCCCAA
Basic information
species | Glycine max |
transcript | GLYMA13G40540.1 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA13G40540.1 (Glycine max), 3'ss of exon 1
lower sequence: Vv06s0004g03680.t01 (Vitis vinifera), 3'ss of exon 1
-----------------------------------------------------------------------------caaaaggtata-gtagtgaaaactgtgactagtactcttgtgttattattattattgggaatgctttgtgt----gatgttaat-tcccttggcttgcttatgcagTATGATGTATATGGAGACCTACTAGGCCTTCTAGGGGCACATCCAGTGTCTCCACTTGTGTCACTTCACCACCTTGATGTAGTGCAACCAATATTCCCAA
| ||||| || ||| || |||| || || || | | | || | | | | | | || | |||| ||||| ||||||||||||| |||||||||||| | |||||||| | || ||||| || ||||| | || ||| ||||||| |||||||||||| | || |||||||||
gttagggcatacaaatccatgggattagaagatgtcaggaattttcatacattctcaaaatcatatctgatgattcctcatttgtatatactgtagaaaggatgtttagtga-ctgaaattggtaccagtttaaactcaactctatatttccaaggatgatgtatcttgttctgcttgtgcagTATGATGTGTATGGAGACCTATTGGGCCTTCTGGCAGCTCATCCTGTAACTCCATTGGTATCAATTCACCATCTTGATGTAGTGGACCCGATATTCCCAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tattattattgggaatgctttgtgtgatgttaattcccttggcttgcttatgcagTATGATGTATATGGAGACCTACTAGGCCTTCTAGGGGCACATCCAGTGTCTCCACTTGTGTCACTTCACCACCTTGATGTAGTGCAACCAATATTCCCAA
tgttaat putative branch site (score: 3)
cttgctt putative PPT
atgttaatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
caaaaggtatagtagtgaaaactgtgactagtactcttgtgttattattattattgggaatgctttgtgtgatgttaattcccttggcttgcttatgcagTATGATGTATATGGAGACCTACTAGGCCTTCTAGGGGCACATCCAGTGTCTCCACTTGTGTCACTTCACCACCTTGATGTAGTGCAACCAATATTCCCAA
- - - - - - - - - -aactgtg
- - - - - - - - - - - - - - - - - tcttgtg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - -gaatgct
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgtgtga