Sequence
atgc intronic sequence ATGC exonic sequence...ataaatttatgcttgtttgataggattgatggattgagcattctcgataaattaataggcattgtggttgggtcaaatgttaattgtttcattcttgcagGTTGATGCAGCTCTTGATTTGAGCCACACACAAAACATAGGGAGAATGATAAAGGCTCACTTTCCGCACTCTCAG
Basic information
species | Glycine max |
transcript | GLYMA13G27210.1 |
intron # | 19 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA13G27210.1 (Glycine max), 3'ss of exon 19
lower sequence: LOC_Os01g67740.1 (Oryza sativa), 3'ss of exon 18
ataaatttatgcttgtttgataggattgatggattgagcattctcgataaattaataggcattgtggttgggtcaaatgttaatt-----gtttcattcttgcagGTTGATGCAGCTCTTGATTTGAGCCACACACAAAACATAGGGAGAATGATAAAGGCTCACTTTCCGCACTCTCAG
| | ||||| | ||| ||| | ||| | || | | || | | ||| || || ||| || ||| | | ||||||||||||| || || ||| ||||||| ||||||||||| || |||||||| ||||| || ||||||||||| |||
---ggctcttcattgtt-aacagggttgttctcttgtaaaagctatgtct-tgaactgaaagtgtctaaagggaaagagttgatgttgtggttcctatactgcagGTTGATGCTGCCCTAGATCTGAGCCATACACAAAACATTGGTAGAATGATCAAGGCGCATTTTCCGCACTCCCAG
upper sequence: GLYMA13G27210.1 (Glycine max), 3'ss of exon 19
lower sequence: GRMZM2G006452_T01 (Zea mays), 3'ss of exon 12
ataaatttatgcttgtttgataggattgatggattgagcattctcgataaattaataggcattgtggttgggt-caaatgttaattgtttcattcttgcagGTTGATGCAGCTCTTGATTTGAGCCACACACAAAACATAGGGAGAATGATAAAGGCTCACTTTCCGCACTCTCAG
|| | | || ||| ||||| ||||| | | | || | | || | ||| | ||| || |||| ||||||||||||| ||||||||| |||||||||| |||||||| || |||||||| |||||||| |||||||||||||||
ttacagtcttgtatgtctgatact-ctgatgcctcaaacgtttgtacggattgtatgctgagagtgaccattttcaactgactgatgttcgtgctctgcagGTTGATGCTGCTCTTGATCTGAGCCACACTCAAAACATTGGTAGAATGATCAAGGCTCATTTTCCGCACTCTCAG
upper sequence: GLYMA13G27210.1 (Glycine max), 3'ss of exon 19
lower sequence: AT3G47460.1 (Arabidopsis thaliana), 3'ss of exon 18
---------------------------------------------------------ataa-atttatgcttgt-ttgataggattgatggattgagcattctcg-ataaattaataggcattgtggttgggtcaaatgttaattgtttcattcttg-cagGTTGATGCAGCTCTTGATTTGAGCCACACACAAAACATAGGGAGAATGATAAAGGCTCACTTTCCGCACTCTCAG
||| || | || |||| || | || | || || || || | | | | ||| | | | || | | || ||| || ||||||||||||||||||||| | ||||||||||| |||||||| ||||||||||| |||| || || || || |||
gtacatctcgattttccatttccatgaatcattgctcttcctttgcattttcaatacgtaacgactaaattcgtgttgacagtgatcttgaaatgttcacaatcacatgatcttgttgagtttgatgacataagagaagtca-tgactttatttttatcagGTTGATGCAGCTCTTGATCTAAGCCACACACAGAACATAGGAAGAATGATAAAATCTCATTTCCCACATTCACAG
upper sequence: GLYMA13G27210.1 (Glycine max), 3'ss of exon 19
lower sequence: AT5G62410.1 (Arabidopsis thaliana), 3'ss of exon 18
--------------------------------------------------------------ataaatttat--gcttgtttgataggattgatggattgagcattctcgataaatta--ataggcattgtggttgggtcaaatgttaattgtttc-attcttgcagGTTGATGCAGCTCTTGATTTGAGCCACACACAAAACATAGGGAGAATGATAAAGGCTCACTTTCCGCACTCTCAG
| || ||| | ||| || || |||| | || || | | |||| || || ||| | |||| | || ||| | | | ||||||||||||||||||||| | || |||||||| |||||||| |||||||||| ||||| || || ||||| |||
gtacatctctgcttttcaatttcagatttctcagtttccaattgatatttcaaattatcatagaagatctatagggttggtttatgtttccgatg--tggaacactgattttgcattacaatcagcga-gtgaagagagaaaatactcatgattttgaattatacagGTTGATGCAGCTCTTGATCTCAGTCACACACAGAACATAGGAAGAATGATAAGAGCTCATTTCCCTCACTCGCAG
upper sequence: GLYMA13G27210.1 (Glycine max), 3'ss of exon 19
lower sequence: PP1S52_57V6.1 (Physcomitrella patens), 3'ss of exon 19
-ataaatttatgcttgtttgataggattgatggattgagcattctcgata-aattaataggcattgtggttgggtcaaatgttaattgtttcat-tcttgcagGTTGATGCAGCTCTTGATTTGAGCCACACACAAAACATAGGGAGAATGATAAAGGCTCACTTTCCGCACTCTCAG
|||| | | || | ||| ||| | | || || || | | || | |||| || ||| || || | |||||||||| || || |||||||||||||| |||||||| |||||||| |||||||| || | |||||||| ||||| |||
cataatccatttcaacctttctgttgcagatctatttaagagaaacggtataaattttcgggacattggtaaaaggaattgtg---tgcttgacgtcttgcagGTGGACGCTGCTCTTGATTTGAGTCACACACAGAACATAGGTAGAATGATCAAAGAACACTTTCCACACTCGCAGMapped EST sequences
Showing partial alignments of ESTs and genomic sequences. See full alignments
ATGC EST sequence
ATGC genomic sequence (exon)
ATGC genomic sequence (truncated intron)
EST:
gi|193393788|gb|FK359865.1|FK359865EST: TTCTGGCACTGCTGCTGTTCAAACCTGCTCCACTTTACATCCTTGATGAG GGTTTGATGCAGCTCTT
genomic: TTCTGGCACTGCTGCTGTTCAAACCTGCTCCACTTTACATCCTTGATGAGgtatgcttta ... attcttgcagG-TT-GATGCAGCTCTT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gataaattaataggcattgtggttgggtcaaatgttaattgtttcattcttgcagGTTGATGCAGCTCTTGATTTGAGCCACACACAAAACATAGGGAGAATGATAAAGGCTCACTTTCCGCACTCTCAG
tgttaat putative branch site (score: 3)
tttcattctt putative PPT
aaatgttaattgttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ataaatttatgcttgtttgataggattgatggattgagcattctcgataaattaataggcattgtggttgggtcaaatgttaattgtttcattcttgcagGTTGATGCAGCTCTTGATTTGAGCCACACACAAAACATAGGGAGAATGATAAAGGCTCACTTTCCGCACTCTCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA
- - - - -tgcttgt
- - - - - - - - - - - - -ttgatgg
- - - - - - - - - - - - - - - - - - -gcattct
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ggttggg