Sequence
atgc intronic sequence ATGC exonic sequencegtgaatggctaagatgcaccttctatttattttatatttttcgttgtttccatgacatgatttcatctgactaaaatttgatgtcctctagatggcccgctctaagaagGCATGCATTGTGTTTTTTGATGAAGTTGATGCAATTGGGGGTGCACGGTTTGATGATGGTGTTGGTGGTGATAATGAGGTTCAGCGCACTATGCTTGAAA
Basic information
species | Glycine max |
transcript | GLYMA03G42370.4 |
intron # | 7 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA03G42370.4 (Glycine max), 3'ss of exon 7
lower sequence: LOC_Os02g54340.2 (Oryza sativa), 3'ss of exon 7
--------------gtgaatggctaagatgcaccttctatttattttatatttttcgt-tgtttccatgacatgatttcatctgactaaaat----ttgatgtcctctagatggcccgctctaagaagGCATGCATTGTGTTTTTTGATGAAGTTGATGCAATTGGGGGTGCACGGTTTGATGATGGTGTTGGTGGTGATAATGAGGTTCAGCGCACTATGCTTGAAA
||||| || | | | || | | || || | | || || | | ||||| | | ||||| |||| |||| | | |||||||||||||| ||||| ||||||||||| || |||||||| |||||||| ||||| ||||| || || |||||||| ||||| ||||||||||||||||
gtatgtgcaacattgtgaa-aactcacaagaacttatcaatt-ttctgcacttaaagtgcttctgtttgacaagcatgtttctgaaaaaaaaaatgttgacttggtttagATGGCCCGCTCGAAGAAAGCATGCATTGTCTTCTTTGATGAGGTTGATGCTATTGGAGGTGCTCGCTTCGATGATGGGGTTGGGGGTGATAATGAGGTTC------------------
upper sequence: GLYMA03G42370.4 (Glycine max), 3'ss of exon 7
lower sequence: GRMZM2G110185_T03 (Zea mays), 3'ss of exon 7
gtgaatggctaaga-tgcaccttctatttattttatatttttcgttgtttccatgacatgatttcatctgactaaaatttgatgtcctctagatggcccgctctaagaagGCATGCATTGTGTTTTTTGATGAAGTTGATGCAATTGGGGGTGCACGGTTTGATGATGGTGTTGGTGGTGATAATGAGGTTCAGCGCACTATGCTTGAAA
|||| || | | || || | |||||| || |||| | ||||| | ||||| | | | | |||||||||||||| ||||||||||||||||| || ||||||||||||||||||||||| ||||| || ||||||||||| ||||||||||| |||||||| |
------ggctgtgaatccgtaaaaggttcatccagtttttttc-ctgcacacatgttaatatttc--tgaaacaaaatattctat--tgtagATGGCCCGCTCAAAGAAGGCATGCATTGTATTCTTTGATGAAGTTGATGCAATTGGTGGTGCTCGTTTTGATGATGGGGTTGGTGGTGACAATGAGGTGC------------------
upper sequence: GLYMA03G42370.4 (Glycine max), 3'ss of exon 7
lower sequence: GRMZM2G110185_T01 (Zea mays), 3'ss of exon 7
----gtgaatggctaaga-tgcaccttctatttattttatatttttcgttgtttccatgacatgatttcatctgactaaaatttgatgtcctctagatggcccgctctaagaagGCATGCATTGTGTTTTTTGATGAAGTTGATGCAATTGGGGGTGCACGGTTTGATGATGGTGTTGGTGGTGATAATGAGGTTCAGCGCACTATGCTTGAAA
| | |||| || | | || || | |||||| || |||| | ||||| | ||||| | | | | |||||||||||||| ||||||||||||||||| || ||||||||||||||||||||||| ||||| || ||||||||||| ||||||||||| |||||||| |
gtatatctagggctgtgaatccgtaaaaggttcatccagtttttttc-ctgcacacatgttaatatttc--tgaaacaaaatattctat--tgtagATGGCCCGCTCAAAGAAGGCATGCATTGTATTCTTTGATGAAGTTGATGCAATTGGTGGTGCTCGTTTTGATGATGGGGTTGGTGGTGACAATGAGGTGC------------------
upper sequence: GLYMA03G42370.4 (Glycine max), 3'ss of exon 7
lower sequence: GRMZM2G181359_T01 (Zea mays), 3'ss of exon 7
----gtgaatggctaagatgcaccttctatttattttatatttttcgttgtttccatgacatgatttcatctgactaaaatttgatgtcctctagatggcccgctctaagaagGCATGCATTGTGTTTTTTGATGAAGTTGATGCAATTGGGGGTGCACGGTTTGATGATGGTGTTGGTGGTGATAATGAGGTTCAGCGCACTATGCTTGAAA
| |||||| || | |||| || | ||||| | || || | ||||| |||| | | |||||||||||||| ||||| || |||||||| || || |||||||||||||| ||||| ||||| || ||||||||||| || ||||| || |||||||| |
gtatatatatggctgtgaatctgtaaatatt-atcccagtcttttcat-gtacgtgtgttcaacatatttctgaaatgaattct-tctatggtagATGGCCCGCTCAAAGAAAGCGTGCATTGTATTCTTCGATGAAGTTGATGCTATTGGTGGTGCTCGTTTTGATGATGGGGTGGGTGGCGACAATGAGGTGC------------------
upper sequence: GLYMA03G42370.4 (Glycine max), 3'ss of exon 7
lower sequence: Vv09s0002g00170.t01 (Vitis vinifera), 3'ss of exon 7
gtgaatggctaagatgcaccttctatttatttt-atatttttcgttgtttcca--tgacatgatttcatctgactaaaatttgatgtc-ctctagatggcccgctctaagaagGCATGCATTGTGTTTTTTGATGAAGTTGATGCAATTGGGGGTGCACGGTTTGATGATGGTGTTGGTGGTGATAATGAGGTTCAGCGCACTATGCTTGAAA
|| | ||| | | | ||| | || || | ||| ||||| || | || |||| | | | | || ||||||| ||||| || || || || |||||||||||||||||||| ||||| || |||||||| || |||||||||||||||||||| || |||||||| |
gtcacaagctgccacatgtttacagtttgtcttcatttattttattgttcttgatcattgctatattgtccgactgctacctttttttgctgcagATGGCACGCTCCAAAAAAGCGTGTATTGTGTTTTTTGATGAAGTAGATGCCATAGGGGGTGCGCGTTTTGATGATGGTGTTGGTGGGGACAATGAGGTCC------------------
upper sequence: GLYMA03G42370.4 (Glycine max), 3'ss of exon 7
lower sequence: PP1S152_13V6.2 (Physcomitrella patens), 3'ss of exon 7
--------------gtgaatggctaagatgcaccttc-tatttattttatatttttcgttgtttccatgacatgatttcatctgactaaaatttgatgtcctctagatggcccgctctaagaagGCATGCATTGTGTTTTTTGATGAAGTTGATGCAATTGGGGGTGCACGGTTTGATGATGGTGTTGGTGGTGATAATGAGGTTCAGCGCACTATGCTTGAAA
| | | | | ||||| || || | || || | | | ||| | || ||| |||| | | ||| | | || | ||||||| || || |||||||| |||||||| ||||||||||| || ||||| ||||| ||||| |||||||| ||||| | || ||||||||||||||||
gtgctaatttattgtttatttgtttagatgaacattagttttcatgtgacgtattttgatgattct----catggtgcaacctgtccatg--ttacttgtgagcagATGGCTCGTTCAAAGAAGGCCTGCATTGTATTTTTTGATGAGGTAGATGCTATTGGAGGTGCTCGGTTTGACGATGGATTGGGGGGTGATAATGAGGTTC------------------
upper sequence: GLYMA03G42370.4 (Glycine max), 3'ss of exon 7
lower sequence: PP1S49_256V6.1 (Physcomitrella patens), 3'ss of exon 7
----------gtgaatggctaagatgc-----accttctatttattttatatttttcgttgttt-ccatgacatgatttcatctgactaaaatttgatgtcctctagatggcccgctctaagaagGCATGCATTGTGTTTTTTGATGAAGTTGATGCAATTGGGGGTGCACGGTTTGATGATGGTGTTGGTGGTGATAATGAGGTTCAGCGCACTATGCTTGAAA
| | || | | || || | |||| | | | |||| || || | || ||||| | | | || ||| | |||||||||| || ||||| || |||||||||||||||||||| || ||||| ||||| ||||| || || || ||||| | || |||||||| |||||||
ccgccagtgtattgtttactcaaacgctaagtactgtgtattcacgtggcctacttcgatgcttatcgtggtgcgattt-gttta--tggaacttgtgagc----agATGGCCCGTTCAAAGAAAGCGTGCATTGTGTTTTTTGATGAGGTAGATGCCATTGGAGGTGCTCGTTTCGACGATGGGTTGGGAGGTGATAACGAGGTTC------------------Mapped 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|209718785|gb|BW671986.1|BW671986EST: TTCAGAAATATGTTGGTGAGGGTGCTCGAATGGTTCGTGAACTATTTCAG GCATGCATTGTGTTTTTTGATGAAGTTGATGCAATTGGGGATGCACGGTTT
genomic: TTCAGAAATATGTTGGTGAGGGTGCTCGAATGGTTCGTGAACTATTTCAGgtgaatggct ... ctctaagaagGCATGCATTGTGTTTTTTGATGAAGTTGATGCAATTGGGGGTGCACGGTTT
EST:
gi|213593731|gb|DB971753.1|DB971753EST: TTCAGAAATATGTTGGTGAGGGTGCTCGAATGGTTCGTGAACTATTTCAG GCATGCATTGTGTTTTTTGATGAAGTTGATGCAATTGGGGATGCACGGTTT
genomic: TTCAGAAATATGTTGGTGAGGGTGCTCGAATGGTTCGTGAACTATTTCAGgtgaatggct ... ctctaagaagGCATGCATTGTGTTTTTTGATGAAGTTGATGCAATTGGGGGTGCACGGTTT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.acatgatttcatctgactaaaatttgatgtcctctagatggcccgctctaagaagGCATGCATTGTGTTTTTTGATGAAGTTGATGCAATTGGGGGTGCACGGTTTGATGATGGTGTTGGTGGTGATAATGAGGTTCAGCGCACTATGCTTGAAA
cccgctct CT-rich tract
taaaatttgat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtgaatggctaagatgcaccttctatttattttatatttttcgttgtttccatgacatgatttcatctgactaaaatttgatgtcctctagatggcccgctctaagaagGCATGCATTGTGTTTTTTGATGAAGTTGATGCAATTGGGGGTGCACGGTTTGATGATGGTGTTGGTGGTGATAATGAGGTTCAGCGCACTATGCTTGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG