Sequence
atgc intronic sequence ATGC exonic sequencegtaagcctgacatttgcatcaacaacatgtctaatattttcttccagtttaattcatttgttaaaattgcaacgttatgtgaaccagGGGAAGCAGAGCATATCATTGGAGCCTGGTGGTCAGTTTGAACTTAGTGGAGCTCCTCTTGAAACCTTGCATCAGACTTGTGCTGAAGTTAATTCCCACC
Basic information
species | Glycine max |
transcript | GLYMA05G37850.3 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA05G37850.3 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os07g27790.1 (Oryza sativa), 3'ss of exon 3
-----------------------------------------------------------------------------------------------------gtaagcctgacatttgcatcaacaacatgtctaatattttctt---ccagtttaattcatttgttaaaatt--gcaacgttatgtgaac-cagGGGAAGCAGAGCATATCATTGGAGCCTGGTGGTCAGTTTGAACTTAGTGGAGCTCCTCTTGAAACCTTGCATCAGACTTGTGCTGAAGTTAATTCCCACC
||| || | | ||||| | || ||| | | | |||| || || |||| | | ||| || ||||| ||||| ||||| ||| | || |||||||||||||||||||||||||| |||||||||||||| || ||||| ||||||||||| || ||||| || |
gtagtattctgctcttatttcccctataataccaccttacatgacttagaccaacaattaacgtggagaaaatttccatgtgcttcactggagtgccgtaattaactctaatggaaaaacaaacaaaaacattacagtttgttctgacaattttagtttgttccttaattcgaggtacttgtatatggttgcagGGAAAGCAAAGCATTTCACTAGAACCTGGTGGTCAGTTTGAACTTAGTGGTGCTCCTCTTGAAACATTACATCAAACTTGTGCTGAGGTCAATTCACATC
upper sequence: GLYMA05G37850.3 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os05g03820.2 (Oryza sativa), 3'ss of exon 3
----------------------------------------------------------------------------gtaagcctgacatttgcatcaacaacatgtc--taatattttcttccagttt-aattcatttgttaaaattgcaacgttatgtgaac-cagGGGAAGCAGAGCATATCATTGGAGCCTGGTGGTCAGTTTGAACTTAGTGGAGCTCCTCTTGAAACCTTGCATCAGACTTGTGCTGAAGTTAATTCCCACC
||| || | | ||||| | | | | |||| || ||| | || || |||| | |||| || ||||| || || ||||| ||| | || ||||| |||||||||||||||||||| |||||||||||||| || ||||| ||||||||||| || ||||| || |
gtagtattcttctgttatttccgctatgagaccaccttacatgacttagaccaacaattaatgtggactgccgtaattaattctaatggagaaacaaacaaaaaaatgacagtttgttctgacaattttagtttatcccttaactcaggctacttatatggttgcagGGAAAACAAAGCATTTCACTAGAACCTGGCGGTCAGTTTGAACTTAGTGGTGCTCCTCTTGAAACATTACATCAAACTTGTGCTGAGGTCAATTCACATC
upper sequence: GLYMA05G37850.3 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G111579_T01 (Zea mays), 3'ss of exon 2
---gtaagcctgacatttgcatcaacaacatgtctaatattttcttccagt--------ttaattcatttgt-taaaattgcaacgttatgtgaac-cagGGGAAGCAGAGCATATCATTGGAGCCTGGTGGTCAGTTTGAACTTAGTGGAGCTCCTCTTGAAACCTTGCATCAGACTTGTGCTGAAGTTAATTCCCACC
| || | || | | | | |||||||| | | | || || | | || || | || | | | |||| ||||| ||||| ||| | || ||||| || || |||||||||||||| |||||||| ||||| || ||||| ||||||||||| || ||||| || |
ttgagatgctacagccaaacacaagttatgcagttttttttttcttctgatggctggcttcagtttatctttgcaaccttacttgtttctacggatgtagGGAAAGCAAAGCATCTCACTAGAACCTGGAGGCCAATTTGAACTTAGTGGCGCTCCTCTCGAAACATTACATCAAACTTGTGCTGAGGTCAATTCGCATC
upper sequence: GLYMA05G37850.3 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G020096_T01 (Zea mays), 3'ss of exon 2
--gtaagcctgacatttgcatcaacaacatgtctaatattttc-------ttccagttt---aattcatttgttaaaattgcaacgtt-atgtgaac-cagGGGAAGCAGAGCATATCATTGGAGCCTGGTGGTCAGTTTGAACTTAGTGGAGCTCCTCTTGAAACCTTGCATCAGACTTGTGCTGAAGTTAATTCCCACC
||| |||| || | | | | | |||| || ||||| | || || | | || || | ||| | || | |||| ||||| ||||| ||| | || ||||| || || |||||||||||||| |||||||| ||||| || ||||| ||||||||||| || || || || |
ctttaaatgccacatccaaatagaaggt-tatgcagttttttaatgatggctctagtttctcagtttatctttgtaacctgaattgtttgtatggatgtagGGAAAGCAAAGCATCTCACTAGAACCTGGAGGCCAATTTGAACTTAGTGGCGCTCCTCTCGAAACGTTACATCAAACTTGTGCTGAGGTCAACTCACATC
upper sequence: GLYMA05G37850.3 (Glycine max), 3'ss of exon 3
lower sequence: AT4G23100.3 (Arabidopsis thaliana), 3'ss of exon 3
----------------------------------------------------------------------gtaagcctgacatttgcatcaacaacatgtctaatattttcttccagtttaattcatttgtt------aaa------attgcaacgttatgtgaaccagGGGAAGCAGAGCATATCATTGGAGCCTGGTGGTCAGTTTGAACTTAGTGGAGCTCCTCTTGAAACCTTGCATCAGACTTGTGCTGAAGTTAATTCCCACC
|| ||| | | || ||| | || || ||| || |||| | || ||| || | | || | || ||| ||||||| ||||| ||||| ||| | || ||||| |||||||| || |||||||| || |||||||| || |||||||| |||||||||||||| ||||| || |
gttaacattctcctgtgtttcatcttttgagccgtttattatttatatacattttcagcctgtagaacatgttagcttcatatacaacacaatgatcggtatattataaggtttcagtcttttttttttttttgctgtagataactcgttctgtccttttgttgaccagGGAAAGCAAAGCATTTCACTTGAACCTGGGGGTCAGTTCGAGCTTAGTGGTGCACCTCTTGAGACTTTGCATCAAACTTGTGCTGAAGTCAATTCACATC
upper sequence: GLYMA05G37850.3 (Glycine max), 3'ss of exon 3
lower sequence: Vv02s0025g03530.t01 (Vitis vinifera), 3'ss of exon 3
------------gtaagcctgac--atttgcatcaacaacatgtctaatattttcttccagtttaattcatttgttaaaattgcaacgttat-gtgaaccagGGGAAGCAGAGCATATCATTGGAGCCTGGTGGTCAGTTTGAACTTAGTGGAGCTCCTCTTGAAACCTTGCATCAGACTTGTGCTGAAGTTAATTCCCACC
| | | | | | || || | | ||| | ||| | || | ||| |||| ||| || |||| || ||||||||||| ||||| ||| |||| || |||||||||||||| ||||| || || ||||||||||| |||||||| || |||||||| |||||||| ||||
ttatcttcaaaggcactcatagctaaggagcttccaagaagtgtttttcgtttattgttggtatgtttctgttgtgaaa--tgtcttattattgttgggcagGGGAAGCAAAGCATCTCACTGGAACCCGGTGGTCAGTTTGAGCTTAGCGGTGCCCCTCTTGAAACTTTGCATCAAACCTGTGCTGAGGTTAATTCACACCMapped 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|213613811|gb|DB961308.1|DB961308EST: TTGACTGGGATAAAGTAATGGAAGGTGATAAAATTATTGGACTCAAACAG GGGAAGCAGAGCATATCA
genomic: TTGACTGGGATAAAGTAATGGAAGGTGATAAAATTATTGGACTCAAACAGgtaagcctga ... tgtgaaccagGGGAAGCAGAGCATATCA
EST:
gi|209707541|gb|BW665000.1|BW665000EST: TTGACTGGGATAAAGTAATGGAAGGTGATAAAATTATTGGACTCAAACAG GGGAAGCAGAGCATATCATTGGAGCCTG
genomic: TTGACTGGGATAAAGTAATGGAAGGTGATAAAATTATTGGACTCAAACAGgtaagcctga ... tgtgaaccagGGGAAGCAGAGCATATCATTGGAGCCTG
EST:
gi|209718854|gb|BW669041.1|BW669041EST: TTGACTGGGATAAAGTAATGGAAGGTGATAAAATTATTGGACTCAAACAG GGGAAGCAGAGCATATCATTGGAGCC
genomic: TTGACTGGGATAAAGTAATGGAAGGTGATAAAATTATTGGACTCAAACAGgtaagcctga ... tgtgaaccagGGGAAGCAGAGCATATCATTGGAGCC
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aatattttcttccagtttaattcatttgttaaaattgcaacgttatgtgaaccagGGGAAGCAGAGCATATCATTGGAGCCTGGTGGTCAGTTTGAACTTAGTGGAGCTCCTCTTGAAACCTTGCATCAGACTTGTGCTGAAGTTAATTCCCACC
agtttaattcatttgt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaagcctgacatttgcatcaacaacatgtctaatattttcttccagtttaattcatttgttaaaattgcaacgttatgtgaaccagGGGAAGCAGAGCATATCATTGGAGCCTGGTGGTCAGTTTGAACTTAGTGGAGCTCCTCTTGAAACCTTGCATCAGACTTGTGCTGAAGTTAATTCCCACC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTCCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG