Sequence
atgc intronic sequence ATGC exonic sequence...gcctttatgtaatatatattgtcatttcaaacccattgacatacacttcactttgtttgttgatttgtatgtaaatattttacttggttttctcttacagGTAATACATTACGATCTTCCCAATTCATCTGAGATATTTGTTCATCGATCTGGACGAACTGGCCGTGCTGGGAAGAAAGGAAGTGCGATTCTTGTTTACA
Basic information
species | Glycine max |
transcript | GLYMA08G41510.1 |
intron # | 6 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA08G41510.1 (Glycine max), 3'ss of exon 6
lower sequence: LOC_Os07g05050.3 (Oryza sativa), 3'ss of exon 4
--------------gcctttatgtaatatatattgtcatttcaaacccattgacata-cacttcactttgtttgttgatttgtatgtaaatattttacttggttttctcttacagGTAATACATTACGATCTTCCCAATTCATCTGAGATATTTGTTCATCGATCTGGACGAACTGGCCGTGCTGGGAAGAAAGGAAGTGCGATTCTTGTTTACA
| ||| | |||| | ||| | | ||| | || | || | | | | || | ||| || | | | | || | ||||| ||||||||||| || || || | || ||| |||||||||| ||||||||||||||| || || ||||||||||||||||| ||| | | ||||
gtaagtagcctgatgtgtttctttaatggaaatttttggaaaagtatgattaatctagctgtttgacgttcatatcggttaacttaaaaa-ataatcttccgcatgcttgttcagGTTATACATTACGAACTCCCAAACACCTCGGAGTTATTTGTTCACAGATCTGGACGAACTGCACGAGCAGGGAAGAAAGGAAGTGCAATTTTAATATACA
upper sequence: GLYMA08G41510.1 (Glycine max), 3'ss of exon 6
lower sequence: GRMZM2G565140_T01 (Zea mays), 3'ss of exon 5
gcctttatgtaatatatatt--gtcatttcaaacccattgacatacacttcactttgtttgttgatttgtatgtaaatattttacttggttttctct-tacagGTAATACATTACGATCTTCCCAATTCATCTGAGATATTTGTTCATCGATCTGGACGAACTGGCCGTGCTGGGAAGAAAGGAAGTGCGATTCTTGTTTACA
| | | | | | | || || | || | || | ||| ||| | | | |||| | | |||| || | | ||||| ||||||| ||| | || ||||| || |||||||| ||||| ||||||| ||||||||||||||||||||||| || | ||| ||| | | ||||
gtttgtgcttccccttctctaagctatctccattattttttgttgcaat-caccatgtgcatcatctgttgtgtac---cctcatgcggttctccttgttcagGTGATACATTTCGAATTGCCAAATTCGTCAGAGATATTCGTTCACAGATCTGGCCGAACTGGCCGTGCTGGGAAGAAGGGCACTGCAATTGTGATGTACA
upper sequence: GLYMA08G41510.1 (Glycine max), 3'ss of exon 6
lower sequence: GRMZM2G107984_T02 (Zea mays), 3'ss of exon 5
gcctttatgtaatatatattgtcatttcaaacccattgacatacacttcactttgtttgttgatttgtatgt-aaatattttact--------tggttttctcttacagGTAATACATTACGATCTTCCCAATTCATCTGAGATATTTGTTCATCGATCTGGACGAACTGGCCGTGCTGGGAAGAAAGGAAGTGCGATTCTTGTTTACA
||| || | | | ||||| || | || |||| ||| || | ||| | | | | |||| || | | || | ||||| ||||||| || | || || || || ||| | |||||||| ||||||| ||||||||||||||||||||||| || | ||| ||| | | ||||
--gtttgtgc------tccccccttctcaaagtcaaagttatctcattcatttttttaatcaccatgtgcatcatctcctctactcctcatattgttctccttgttcagGTGATACATTTTGAATTGCCAAACTCGTCAGAGTTGTTTGTTCACAGATCTGGCCGAACTGGCCGTGCTGGGAAGAAGGGCACTGCAATTGTGATGTACA
upper sequence: GLYMA08G41510.1 (Glycine max), 3'ss of exon 6
lower sequence: AT3G22310.1 (Arabidopsis thaliana), 3'ss of exon 5
gcctttatgtaatatatattgtcatttcaaacccattgacatacacttcactttgtttgttgatttgtatgtaaatattttacttggttttctcttacagGTAATACATTACGATCTTCCCAATTCATCTGAGATATTTGTTCATCGATCTGGACGAACTGGCCGTGCTGGGAAGAAAGGAAGTGCGATTCTTGTTTACA
| || | || | | | ||| ||| | |||| | | | | || | || | | ||| | | ||||||||| ||||| || ||||| ||| | |||| |||||||| ||| | || |||||||| |||||||| ||||||||||| |||||||| | ||
-----------------gtgagtgaaaacaataccttttcttgcgcttaactagttctgtttctcattttattaac-ctgtattgtgctttgtgt-acagGTAATTCATTATGAGCTTCCTAATAACACGGAGACGTTTGTTCACCGAACGGGGCGAACTGGTCGTGCTGGAAAGAAAGGAAGCGCGATTCTCATCCACG
upper sequence: GLYMA08G41510.1 (Glycine max), 3'ss of exon 6
lower sequence: Vv12s0142g00670.t01 (Vitis vinifera), 3'ss of exon 5
-gcctttatgtaatatatattgtcatttcaaacccattgacatacacttcactttgtttgttgat-ttgtatgtaaatattttacttggttttctcttacagGTAATACATTACGATCTTCCCAATTCATCTGAGATATTTGTTCATCGATCTGGACGAACTGGCCGTGCTGGGAAGAAAGGAAGTGCGATTCTTGTTTACA
| | | | | | | || |||||| | | | | | || || | | | | | | | || | |||||| ||| |||||||||| || ||||||||||| || ||||| ||||||||||| ||||||||||| || ||||| || |||||||||| ||| ||||| ||||
tttttgtttccattctttcacttcttttcaacactttccaaagctatgcatgttcacatgccgttgctttttcttcacatgccgttc--ttttcttgctcagATAATACATTATGAGCTTCCCAATTCCTCAGAGATCTTTGTTCATCGGTCTGGACGAACAGGACGTGCAGGAAAGAAAGGAACTGCAATTCTCATTTATG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.cttcactttgtttgttgatttgtatgtaaatattttacttggttttctcttacagGTAATACATTACGATCTTCCCAATTCATCTGAGATATTTGTTCATCGATCTGGACGAACTGGCCGTGCTGGGAAGAAAGGAAGTGCGATTCTTGTTTACA
tgttgat putative branch site (score: 4)
cttggttttctctt putative PPT
tttgttgatttgtatg 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gcctttatgtaatatatattgtcatttcaaacccattgacatacacttcactttgtttgttgatttgtatgtaaatattttacttggttttctcttacagGTAATACATTACGATCTTCCCAATTCATCTGAGATATTTGTTCATCGATCTGGACGAACTGGCCGTGCTGGGAAGAAAGGAAGTGCGATTCTTGTTTACA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA
gccttta
- - - - - - - - - - - - - tcaaacc
- - - - - - - - - - - - - - - - - - - acataca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgttgat
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgtatgt