Sequence
atgc intronic sequence ATGC exonic sequence...tttctgattttggaatctgattgcccatacttattttttgctggagacacttgtttggatgtgctgaagactgtatttgactttttcatatatgcttcagGTATGAGGAGGGCTACAGGGGGCAGTTGGTTATCTGTAAGTCAAGGGATAGCAGAGGATACATCTGATCTTGTATCAGGATTTGCTACAGTTGGTGATGG
Basic information
species | Glycine max |
transcript | GLYMA05G33560.1 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA05G33560.1 (Glycine max), 3'ss of exon 1
lower sequence: LOC_Os03g51020.1 (Oryza sativa), 3'ss of exon 1
tttctgattttggaatctgattgcccatacttattttttgctggagacacttgtttggatgtgctgaagactgta--tttgactttttcatatatgc-ttcagGTATGAGGAGGGCTACAGGGGGCAGTTGGTTATCTGTAAGTCAAGGGATAGCAGAGGATACATCTGATCTTGTATCAGGATTTGCTACAGTTGGTGATGG
| ||| || | || ||||| | ||| || || | |||||| | | ||| | | |||| | | | || ||||||| || | | | | | ||||| ||||| |||||||| || ||||||||||| ||||| | ||||| || ||||| ||| |||||||||
atagtgaaattata-tcagattgttttccatgattcttagcctctctga--tgtttgatgctacataagtttttgaccttgaactatatgtttacaaattcagGTGGAAGACGCACAATTAGTAATAACTGGTTCTCTGTCAGTCAAGGTATTGCAGAGGATACTTCTGACTTGGTATCGGGCTTTGCAACAATTGGTGATGA
upper sequence: GLYMA05G33560.1 (Glycine max), 3'ss of exon 1
lower sequence: AT1G73460.1 (Arabidopsis thaliana), 3'ss of exon 1
-----tttctgattttggaatctgattgcccatacttattttttgctggagacacttgtttggatgtgctgaagactgtatttgactttttcatatatgcttcagGTATGAGGAGGGCTACAGGGGGCAGTTGGTTATCTGTAAGTCAAGGGATAGCAGAGGATACATCTGATCTTGTATCAGGATTTGCTACAGTTGGTGATGG
||| || | | | || |||| || | | || || | |||| ||| || || || | ||| | | |||| || | |||| ||||| | ||| | || |||||||| || ||||||||||| ||||||||||||| || || |||||||| ||||||||||
tgtcgcttcactttctactttttttttagttcaacttgaaccttaccagttttac---ttcaggtgtg--aaagtaagttttaatctcctaattatttcatatagGTGGGAAAAAATCTACTGGGGGAAACTGGCTTTCAGTAAGTCAGGGAATAGCAGAGGACGCATCTGATCTTGTTTCGGGTTTTGCTACTATTGGTGATGG
upper sequence: GLYMA05G33560.1 (Glycine max), 3'ss of exon 1
lower sequence: Vv01s0011g01590.t01 (Vitis vinifera), 3'ss of exon 6
--tttctgattttggaatctgattgcccatacttattttttgctggagacacttgtttggatgtgctgaagactgtatttgactttttcatatatgcttcagGTATGAGGAGGGCTACAGGGGGCAGTTGGTTATCTGTAAGTCAAGGGATAGCAGAGGATACATCTGATCTTGTATCAGGATTTGCTACAGTTGGTGATGG
| | | || | | | | || || | | | ||| |||| |||| | | |||| || | | | || | ||| |||||| | | | | |||||||||||| |||||||||||||||| || ||||||||||| |||||||| || || || |||||||| |||||||| ||
gatgtttcatgt--gttttttatgccctgttatgcatctttctgagagatttccttttgtaaaccgtaaagaatgagccttattcttgaaatgatgactcagGTGGAAAACGAACAGCTGGGGGCAGTTGGCTATCTGTAAGTCAAGGCATTGCAGAGGATACCTCTGATCTGGTTTCTGGTTTTGCTACTGTTGGTGACGG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gacacttgtttggatgtgctgaagactgtatttgactttttcatatatgcttcagGTATGAGGAGGGCTACAGGGGGCAGTTGGTTATCTGTAAGTCAAGGGATAGCAGAGGATACATCTGATCTTGTATCAGGATTTGCTACAGTTGGTGATGG
atttgac putative branch site (score: 4)
actttttcatatat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tttctgattttggaatctgattgcccatacttattttttgctggagacacttgtttggatgtgctgaagactgtatttgactttttcatatatgcttcagGTATGAGGAGGGCTACAGGGGGCAGTTGGTTATCTGTAAGTCAAGGGATAGCAGAGGATACATCTGATCTTGTATCAGGATTTGCTACAGTTGGTGATGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAT
- - - - - - - - ctgattg
- - - - - - - - - - - -cccatac
- - - - - - - - - - - - - - - - - - - tgctgga
- - - - - - - - - - - - - - - - - - - - - - - -cacttgt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgctgaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gactgta