Sequence
atgc intronic sequence ATGC exonic sequence...aattaatccaaatcaatctagaaatacagattgctgaagctgcattttaaagtttctttattctgcttgtcatatgatcactgttttttgtttttcttagATTCGTCCAGATCGTCAAACTTTGTATTGGAGTGCTACCTGGCCAAAGGAGGTCGAACAATTGGCAAGGAAGTTCCTTTATAACCCATACAAA
Basic information
species | Glycine max |
transcript | GLYMA07G11880.1 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA07G11880.1 (Glycine max), 3'ss of exon 5
lower sequence: LOC_Os01g10050.1 (Oryza sativa), 3'ss of exon 5
----aattaatccaaatca--atctagaaatacagattgctgaagctgcattttaaagtttctttattctgcttgtcatatgatcactgttttttgtttttcttagATTCGTCCAGATCGTCAAACTTTGTATTGGAGTGCTACCTGGCCAAAGGAGGTCGAACAATTGGCAAGGAAGTTCCTTTATAACCCATACAAA
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cactgcccagccataggcagagttttcctccatgaaccgtgcctacaacataccaacattgttttacatag--tgttaagggattaccatctgcc----ttttcagATTCGTCCAGATCGCCAAACATTATATTGGAGTGCTACTTGGCCAAAGGAAGTTGAACAGCTAGCAAGGAACTTTCTTTTCGACCCATACAAG
upper sequence: GLYMA07G11880.1 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM2G143246_T01 (Zea mays), 3'ss of exon 5
-aattaatccaaatcaatctagaaatacagattgctgaagc-tgcattttaaagtttctttattctgcttgtcatatgatcactgttttttgtttttcttagATTCGTCCAGATCGTCAAACTTTGTATTGGAGTGCTACCTGGCCAAAGGAGGTCGAACAATTGGCAAGGAAGTTCCTTTATAACCCATACAAA
| | || | || || | | | | | | |||| | |||| ||| ||||| | || ||| | || | |||| | | |||||||||||||||| ||||| | || ||||||||||||||||| ||||| || || || | |||||||| ||||||| | ||||||||||
ttagtggtctacattgatatgccagttactttcattaatctgtgcaatataaattttgattattgt-tttacgtgatgccaaaccttatctgttagt-tcagATTCGTCCAGATCGCCAAACACTTTACTGGAGTGCTACCTGGCCGAAGGAAGTTGAGCAGCTAGCAAGGAATTTCCTTTTTGACCCATACAAG
upper sequence: GLYMA07G11880.1 (Glycine max), 3'ss of exon 5
lower sequence: AT1G55150.1 (Arabidopsis thaliana), 3'ss of exon 5
aattaatccaaatcaatctagaaatacagattgctgaagctg-cattttaaagtttctttattctgcttgtcatatgatcactgttttttgtttttcttagATTCGTCCAGATCGTCAAACTTTGTATTGGAGTGCTACCTGGCCAAAGGAGGTCGAACAATTGGCAAGGAAGTTCCTTTATAACCCATACAAA
| ||| | | ||| | ||| | | || | | ||||| ||| | | | ||||| | ||||||| ||||| |||||||||||||| |||||||| || ||||| |||||||| |||||| | | | |||||| ||||||||||||||||||
-----------------gttcgtttacttactcctgtcttcgtcatatatatgtgtatgctagttgctttgtctataacctttctttttaaacctgtgcagATTCGGCCAGACCGTCAAACTTTGTACTGGAGTGCCACTTGGCCTAAGGAGGTGGAACAACTATCGAAGAAGTTTCTTTATAACCCATACAAA
upper sequence: GLYMA07G11880.1 (Glycine max), 3'ss of exon 5
lower sequence: Vv09s0002g02100.t01 (Vitis vinifera), 3'ss of exon 5
aattaatccaaatcaatctagaaatacagattgctgaagctgcattt--taaagtttctttattctgct--tgtcatatgatcactgttt--tttgtttttcttagATTCGTCCAGATCGTCAAACTTTGTATTGGAGTGCTACCTGGCCAAAGGAGGTCGAACAATTGGCAAGGAAGTTCCTTTATAACCCATACAAA
|||| | | || | | || | || || | | || | | || |||| | ||| | | | || |||| ||| ||||||||||| ||||||||||| | |||||||||||||| ||||| |||||||| |||||| | || |||||||||||||| ||||||| |||
-----atccggctta-cctttctcctctcttccttgtaattgtatctgttgaattctgcataatctggagatatcaggttcctatttattggtttgctttatgtagATTCGTCCTGATCGTCAAACCCTCTATTGGAGTGCTACATGGCCCAAGGAGGTGGAACAACTTGCTAGGAAGTTCCTTTACAACCCATGTAAAMapped 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|8401669|gb|BE057303.1|BE057303EST: GATGTTGGATATGGGGGTTTGATCCTCAGCTACGGAAGATTGTCTCCCAG ATTCGTCCAGATCGTCAAACTTTGTATTGGAGTGCTACCTGGCCAAAGGAA
genomic: GATGTTGGATATGGGG-TTTGATCCTCAGCTACGGAAGATTGCCTCCCAGgttggcttta ... tttttcttagATTCGTCCAGATCGTCAAACTTTGTATTGGAGTGCTACCTGGCCAAAGGAG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tttaaagtttctttattctgcttgtcatatgatcactgttttttgtttttcttagATTCGTCCAGATCGTCAAACTTTGTATTGGAGTGCTACCTGGCCAAAGGAGGTCGAACAATTGGCAAGGAAGTTCCTTTATAACCCATACAAA
tcactgttttttgttt CT-rich tract
ttttttgtttttctta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
aattaatccaaatcaatctagaaatacagattgctgaagctgcattttaaagtttctttattctgcttgtcatatgatcactgttttttgtttttcttagATTCGTCCAGATCGTCAAACTTTGTATTGGAGTGCTACCTGGCCAAAGGAGGTCGAACAATTGGCAAGGAAGTTCCTTTATAACCCATACAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA
- - -atccaaa
- - - - - - - - - - gaaatac
- - - - - - - - - - - - - - - -tgctgaa
- - - - - - - - - - - - - - - - - - - - tgcattt