Sequence
atgc intronic sequence ATGC exonic sequence...tcctaaaatttcttgggagtttcatattcgttgattgtatatgttttaatcaatggtttagagcaacatcttcaaatcttccctgccatttatatttcagGGTCCACGAATGGTTCGTGATGTATTTCGTCTCGCTAAAGAGAATGCGCCTGCAATTATATTTATTGATGAGGTTGATGCAATAGCCACGGCTAGATTTG
Basic information
species | Glycine max |
transcript | GLYMA11G31450.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA11G31450.1 (Glycine max), 3'ss of exon 2
lower sequence: LOC_Os02g21970.1 (Oryza sativa), 3'ss of exon 2
tcctaaaatttcttgggagtttcatattcgttgattgtatatgttttaatcaatggtttag-agcaacatcttcaaatcttccctgccatttatat-ttcagGGTCCACGAATGGTTCGTGATGTATTTCGTCTCGCTAAAGAGAATGCGCCTGCAATTATATTTATTGATGAGGTTGATGCAATAGCCACGGCTAGATTTG
|| | |||| ||| |||||| | | | | | | | || || || | | | || ||| || | || |||| || | |||||||| |||||||| ||| | |||||||||||||| || || || ||||| || |||||||||||||| ||||| || ||| | ||||
--gctttatgttttggatgttgagacttcgtttgtagattttctatggtttttgggcatactagttcttttcttgatgaagttcttttattcatttgtttagGGACCTAGGATGGTTCGAGATGTATTCCGTTTGGCTAAAGAGAATGCCCCAGCTATCATATTCATCGATGAGGTTGATGCTATAGCAACTGCTCGTTTTG
upper sequence: GLYMA11G31450.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G038126_T01 (Zea mays), 3'ss of exon 2
tcctaaaatttcttgggagtttcatattcgttgattgtatatgttttaatcaatggtttagag----caacatcttcaaatcttccctgccatttatatttcagGGTCCACGAATGGTTCGTGATGTATTTCGTCTCGCTAAAGAGAATGCGCCTGCAATTATATTTATTGATGAGGTTGATGCAATAGCCACGGCTAGATTTG
|| || || | || | || || || || | | || | | | ||| | |||||| | || | | | | || |||| || ||||||| |||||||| || ||| | ||||| |||||||| || ||||| || || ||||||||||||||||| |||||||| ||| | ||||
--ttagtggttattcgtagatatatgtt-gtcgacataaaaatttgcagttccttttttcggctgttcaacattagtcagtcatattcttaactcct-ttgtagGGCCCTAGAATGGTGCGTGATGTGTTCCGTTTGGCTAAGGAGAATGCTCCAGCAATCATTTTCATTGATGAGGTTGATGCTATAGCCACTGCTCGCTTTG
upper sequence: GLYMA11G31450.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G090904_T01 (Zea mays), 3'ss of exon 2
tcctaaaatttcttgggagtttcatattcgttgattgtatatgttttaatcaatggtttagagcaacatcttcaaatctt----ccctgccatttatatttcagGGTCCACGAATGGTTCGTGATGTATTTCGTCTCGCTAAAGAGAATGCGCCTGCAATTATATTTATTGATGAGGTTGATGCAATAGCCACGGCTAGATTTG
||| | | ||| ||| || || | | | ||||| | || | | |||| | | || | | | | || | || |||| || ||||||| ||||| || || ||| | || || |||||||| || ||||| || || ||||||||||||||||| |||||||| ||| | ||||
-cctgtcgtggacataaaattttgcatttttttcttcttttcagct-gttcaatatatcagtcctat-tcttgacgtgttatgatctttctacttct-ttgtagGGCCCTAGAATGGTGCGTGACGTGTTCCGTTTGGCCAAGGAGAATGCCCCAGCAATCATTTTCATTGATGAGGTTGATGCTATAGCCACTGCTCGTTTTG
upper sequence: GLYMA11G31450.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv06s0004g08220.t01 (Vitis vinifera), 3'ss of exon 2
-tcctaaaatttcttgggagtttcatattcgttgattgtatatgttttaatcaatggtttagagcaacatcttcaaatcttccctgccatttatatttcagGGTCCACGAATGGTTCGTGATGTATTTCGTCTCGCTAAAGAGAATGCGCCTGCAATTATATTTATTGATGAGGTTGATGCAATAGCCACGGCTAGATTTG
| |||| || |||| | | || | || || | ||| | | | | | || || | | || | | ||||||| ||||||| |||||||| || ||||| || || |||||||| ||||||||||| || ||||||||||||||||| || || || ||||| ||||
tggttttaattgttttatcttttctagattgccaatattgc-tgcaatacccttaaattttaatttatctatatatatattttttttctcttgttatcaagGGTCCGAGAATGGTCCGTGATGTTTTCCGTCTTGCCAAGGAGAATGCTCCTGCAATTATCTTCATTGATGAGGTTGATGCTATTGCTACCGCTAGGTTTG
upper sequence: GLYMA11G31450.1 (Glycine max), 3'ss of exon 2
lower sequence: PP1S147_100V6.1 (Physcomitrella patens), 3'ss of exon 2
---tcctaaaatttcttgggagtttcatattcgttgattgtatatgttttaatcaatggtttagagcaacatcttcaaatcttccctgccatttatatttcagGGTCCACGAATGGTTCGTGATGTATTTCGTCTCGCTAAAGAGAATGCGCCTGCAATTATATTTATTGATGAGGTTGATGCAATAGCCACGGCTAGATTTG
| || ||| ||| | || | || || |||||| || | | || || | | | | |||| | || || | |||| |||||||| || ||||| ||||||||||||| || || || || ||||| || || ||||||||||||||||| |||||||||| || || || | || |
gtattttatgcactctcaggaaacgtagttttga-aatggtctatgttataggacgtcggtt-gaactatgtttgagtatctcgcatgtaatgt-tattacagGGTCCCCGTATGGTGCGTGATGTATTTCAACTGGCAAAGGAAAATGCCCCAGCTATTATATTTATTGATGAAATTGATGCAATCGCAACAGCCCGTTTCG
upper sequence: GLYMA11G31450.1 (Glycine max), 3'ss of exon 2
lower sequence: PP1S36_183V6.1 (Physcomitrella patens), 3'ss of exon 2
tcctaaaatttcttgggagtttcatattcgttgattgtatatgttttaatcaatggtttagag-caacatcttcaaatcttccctgccatttatatttcagGGTCCACGAATGGTTCGTGATGTATTTCGTCTCGCTAAAGAGAATGCGCCTGCAATTATATTTATTGATGAGGTTGATGCAATAGCCACGGCTAGATTTG
| | | |||| | | | | || || || | | || ||| || | || | || || | |||| |||||||| || ||||| ||||||||||| ||||| || || |||||||| || || |||||||||||||||||| |||||||||| || || ||| | ||||
ttatgttgcaagataatcctttcgtttctggtaatcaatcattttaaaccctcgggcttattttcagcttcacttgaactcatgtgtagcct-tattacagGGTCCCCGTATGGTGCGTGATGTATTCCGTCTAGCGAAGGAGAATGCCCCAGCCATTATATTTATTGATGAGATTGATGCAATTGCAACAGCTCGTTTTGMapped 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|16284036|gb|BI945871.1|BI945871EST: CCTTCATCAGGGTTGTGGGATCTGAGTTTGTGCAGAAGTATCTTGGTGAG GGTCCACGAATGGTTCGTGATGTATTTCGTCTCGCTAAAGAGAATGCGCCT
genomic: CCTTCATCAGGGTTGTGGGATCTGAGTTTGTGCAGAAGTATCTTGGTGAGgtatgatttt ... tatatttcagGGTCCACGAATGGTTCGTGATGTATTTCGTCTCGCTAAAGAGAATGCGCCT
EST:
gi|17152954|gb|BM142887.1|BM142887EST: CCTTCTTCAGGGTTGTGGGATCTGAGTTTGTGCAGAAGTATCTTGGTGAG GGTCCACGAATGGTTCGTGATGTATTTCGTCTCGCTAAAGAGAATGCGCCT
genomic: CCTTCATCAGGGTTGTGGGATCTGAGTTTGTGCAGAAGTATCTTGGTGAGgtatgatttt ... tatatttcagGGTCCACGAATGGTTCGTGATGTATTTCGTCTCGCTAAAGAGAATGCGCCT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttaatcaatggtttagagcaacatcttcaaatcttccctgccatttatatttcagGGTCCACGAATGGTTCGTGATGTATTTCGTCTCGCTAAAGAGAATGCGCCTGCAATTATATTTATTGATGAGGTTGATGCAATAGCCACGGCTAGATTTG
ttttaat putative branch site (score: 3)
tcttccctgccattt putative PPT
atttatatttca 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tcctaaaatttcttgggagtttcatattcgttgattgtatatgttttaatcaatggtttagagcaacatcttcaaatcttccctgccatttatatttcagGGTCCACGAATGGTTCGTGATGTATTTCGTCTCGCTAAAGAGAATGCGCCTGCAATTATATTTATTGATGAGGTTGATGCAATAGCCACGGCTAGATTTG
- - - - - - ttgggag
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - catcttc