Sequence
atgc intronic sequence ATGC exonic sequencegtatcaatcaattgtgtttcggattaggctaattatgtttgattttatagatgatatgcacaattctattttatgtatgtaaaaacaaattacactgttttgcctttcagGTTTGGTCCATACTTTTGCCAGCCTGTAATTGCTGGACTAGGAGATGATGACAAGCCATTCATTTGCACAATGGATGCCATTGGAGCAAA
Basic information
species | Glycine max |
transcript | GLYMA06G11930.1 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA06G11930.1 (Glycine max), 3'ss of exon 1
lower sequence: LOC_Os06g43570.1 (Oryza sativa), 3'ss of exon 4
gtatcaatcaattgtgtttcggattaggctaatt-atgtttgattttatagatgatatgcacaattctattttatgtatgtaaaaacaaattacactgttttgcctttcagGTTTGGTCCATACTTTTGCCAGCCTGTAATTGCTGGACTAGGAGATGATGACAAGCCATTCATTTGCACAATGGATGCCATTGGAGCAAA
|| | | || | || | || || || ||| || | | | | | ||||| || | | | |||| | ||||| ||||| |||||||| ||||||||||| || |||||||| ||||| || | ||||||| ||||| || ||||| |||||| |||||
-----tctctgtgctattagtaaacagctttcttcattttgtattatacaattattgggttaggggtaagtttatctaacttttttcga--tacatgg----aaaattcagATTTGGACCATACTTCTGCCAGCCTGTTATCGCTGGACTTGGAGAGGACAATGAGCCATTTATTTGTACCATGGACTGCATTGGTGCAAA
upper sequence: GLYMA06G11930.1 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G045371_T02 (Zea mays), 3'ss of exon 3
gtatcaatcaattgt-gtttcggattaggctaattatgtttgattttatagatgatatgcacaattctattttatgtatgtaaaaacaaattacactgttttgc-ctttcagGTTTGGTCCATACTTTTGCCAGCCTGTAATTGCTGGACTAGGAGATGATGACAAGCCATTCATTTGCACAATGGATGCCATTGGAGCAAA
| ||| || || ||| ||||| | ||||||| | ||| | || |||| | | | ||| | || || | | | ||||||| ||||| ||||| || |||||||| || ||||||||||| |||||||| || ||||||||||| || ||||| | | || |||||
---ttaattcatagttacttcaaattagctt--ttatgttcaa----atactggtactgattaattgcaatgtttgtct---aacttttatcatgccacatgaaactttcagATTTGGGCCATATTTCTGCCAGCCAGTCATTGCTGGACTTGGAGATGACAACGTACCATTCATTTGTACCATGGACTGCCTCGGTGCAAA
upper sequence: GLYMA06G11930.1 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G092975_T01 (Zea mays), 3'ss of exon 3
gtatcaatcaattgt-gtttcggattaggctaattatgtttgatt-ttatagatgatatgcacaat-tctattttatgtatgtaaaaacaaattacactgttttgcctttcagGTTTGGTCCATACTTTTGCCAGCCTGTAATTGCTGGACTAGGAGATGATGACAAGCCATTCATTTGCACAATGGATGCCATTGGAGCAAA
| |||| | || | | | ||||| | |||| || | | | | | || |||| | | ||| | | | | | ||| || | ||| ||||| || || ||||| ||||||||||| || ||||||||||| |||||||| || ||||| ||||| || ||||| | | || |||||
--cttaatccgtagttgctgcaaattagctt--ttatcttcaaatactgaaactttcattggcaatgtttgtttaacttttatcatgacacatgaaact---------ttcagATTCGGGCCATATTTTTGCCAGCCAGTCATTGCTGGACTTGGAGATGACAACGTACCATTTATTTGTACTATGGACTGCTTAGGTGCAAA
upper sequence: GLYMA06G11930.1 (Glycine max), 3'ss of exon 1
lower sequence: AT1G77440.1 (Arabidopsis thaliana), 3'ss of exon 3
gtatcaatcaattgtgtt----tcggattaggctaattatgtttgattt--tatagatgatatgcacaattctattttatgta----tgtaaaaacaaattacactgttttgcctttcagGTTTGGTCCATACTTTTGCCAGCCTGTAATTGCTGGACTAGGAGATGATGACAAGCCATTCATTTGCACAATGGATGCCATTGGAGCAAA
| | || ||| || || | | | || | | | | ||| | | | || || || | || |||| || | || || ||| || | |||||| ||||| |||| ||| ||||| ||||| ||||||||| | ||||||||| |||| || ||||||||||| |||||| | |||||||| ||
--gttggtgaaatgtcttcttctctcaatttgttattagtttctagtttcctcttaacaatctgatttcttatgattaatgtggcattgccactactaagtaccaaattctttatttcagATTTGGCCCATTCTTGTGCCAACCTGTGATTGCTGGATTGGGAGATGATAACAAACCCTTCATTTGCACTATGGATTCTATTGGAGCCAA
upper sequence: GLYMA06G11930.1 (Glycine max), 3'ss of exon 1
lower sequence: AT1G21720.1 (Arabidopsis thaliana), 3'ss of exon 3
--------------------------------------------gtatcaatcaattgtgtttcggattaggctaattatgtttgattttatagatgatatgcacaattctattttatgt----atgtaaaaaca-aattacactgttt--tgcctttcagGTTTGGTCCATACTTTTGCCAGCCTGTAATTGCTGGACTAGGAGATGATGACAAGCCATTCATTTGCACAATGGATGCCATTGGAGCAAA
| | || || | | | | ||| || | || ||| ||||| ||| | || | | | || || ||| | ||| | | || || | |||||| |||||||| ||||| ||||| ||||| |||||||| | ||||||||||||||||| ||||||||||| ||||| | || ||||| ||
gtcagtgtgcttgtgttgtttacttatgtagctgtattagttacctgttgatttgcgatgctgcttctgactctagttttaattctggttaggaatgatttgcttagtttgtctctgaatcatgatttagaaagataatcagattggttgctttatttcagATTTGGTCCTTACTTATGCCAACCTGTGATTGCTGGCTTGGGAGATGATGACAAGCCTTTCATTTGCACGATGGACTCTATCGGAGCCAA
upper sequence: GLYMA06G11930.1 (Glycine max), 3'ss of exon 1
lower sequence: Vv18s0001g02260.t01 (Vitis vinifera), 3'ss of exon 3
gtatcaatcaattgtgtttcggattaggctaattatgtttgattttatagatgatatgcacaattctattttatgtatgtaaaaacaaattacactgttttgcctttcagGTTTGGTCCATACTTTTGCCAGCCTGTAATTGCTGGACTAGGAGATGATGACAAGCCATTCATTTGCACAATGGATGCCATTGGAGCAAA
|||| | || || || | |||| | | | ||||| | | | | | | | | | || | || |||||| ||| ||||||||||||||||| ||||||||||| ||||||||| | |||||||| ||||||||||||||||||||||||||| | |||||||| ||
-catcattgtcaccctccctttataagcactgttttctttggtgtc-tgtatgatttcaatgaagatgatatgcatttctgaatataa-------tgtttt-ttttttagGTTTGGTCCATACTTCTGCCAGCCTGTGATTGCTGGATTGGGAGATGAAGACAAGCCATTCATTTGCACAATGGATTCAATTGGAGCCAA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.atgcacaattctattttatgtatgtaaaaacaaattacactgttttgcctttcagGTTTGGTCCATACTTTTGCCAGCCTGTAATTGCTGGACTAGGAGATGATGACAAGCCATTCATTTGCACAATGGATGCCATTGGAGCAAA
ctgttttgcctttc CT-rich tract
aattctattttatgta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatcaatcaattgtgtttcggattaggctaattatgtttgattttatagatgatatgcacaattctattttatgtatgtaaaaacaaattacactgttttgcctttcagGTTTGGTCCATACTTTTGCCAGCCTGTAATTGCTGGACTAGGAGATGATGACAAGCCATTCATTTGCACAATGGATGCCATTGGAGCAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCA