Sequence
atgc intronic sequence ATGC exonic sequence...tactttacattaaaagattgtgtttcttatggggatgctgttgataatgtcaaagtgcaacttttatttggaatcatcatttatttgtctggtaatgcagTGGATGCGTCACATCAGCAGAGACAGTTATGCTGGAGAAGCAAAGTTTGGATGAGTTTCTGAACAATATTAATTCAGGAAAGGCCGTGATTGTGTCTCTT
Basic information
species | Glycine max |
transcript | GLYMA17G01120.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA17G01120.1 (Glycine max), 3'ss of exon 2
lower sequence: LOC_Os03g53750.1 (Oryza sativa), 3'ss of exon 2
tactttacattaaaagattgtgtttcttatggggatgctgttgataatgtcaaagtgcaacttttatttggaatcatcatttatttgtctggtaatgcagTGGATGCGTCACATCAGCAGAGACAGTTATGCTGGAGAAGCAAAGTTTGGATGAGTTTCTGAACAATATTAATTCAGGAAAGGCCGTGATTGTGTCTCTT
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--gttttctttactaccttgcactgttcattcaatca--gcagct--tgtccaaatccaaataatgct---gactgt--ttcattt---taatcccatagTGGTTGCATAACATCAGCAGAAACAGTTATGCTTGAGAAGCAAAGCTTGGGTGACTTCATTACTCGCATCAACTCTGACAAAGCTGTCATAGTATCGGTC
upper sequence: GLYMA17G01120.1 (Glycine max), 3'ss of exon 2
lower sequence: LOC_Os03g53750.2 (Oryza sativa), 3'ss of exon 2
tactttacattaaaagattgtgtttcttatggggatgctgttgataatgtcaaagtgcaacttttatttggaatcatcatttatttgtctggtaatgcagTGGATGCGTCACATCAGCAGAGACAGTTATGCTGGAGAAGCAAAGTTTGGATGAGTTTCTGAACAATATTAATTCAGGAAAGGCCGTGATTGTGTCTCTT-----------------
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--gttttctttactaccttgcactgttcattcaatca--gcagct--tgtccaaatccaaataatgct---gactgt--ttcattt---taatcccatagtggttgcataacatcagCAGAAACAGTTATGCTTGAGAAGCAAAGCTTGGGTGACTTCATTACTCGCATCAACTCTGACAAAGCTGTCATAGTATCGGTCTCTCCACAGTCAAGAGC
upper sequence: GLYMA17G01120.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G171998_T01 (Zea mays), 3'ss of exon 2
tactttacattaaaagattgtgtttcttatggggat--gctgttgataatgtcaaagtgcaacttttatttggaatcatcatttatttgtctggtaatgcagTGGATGCGTCACATCAGCAGAGACAGTTATGCTGGAGAAGCAAAGTTTGGATGAGTTTCTGAACAATATTAATTCAGGAAAGGCCGTGATTGTGTCTCTT
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-gtttttcttttattttctttttttactcttttgatcagttgtcaataagtaacctgatcaatttcaatc---aatgctgactgattcatctt-tgtcttagTGGTTGTATAACATCGGCAGAGACGGTTATGCTGGAGAAGCAAAGCTTGGGTGACTTCATTGATCGTATAAACTCTGATAAAGCTGTTATTGTATCTGTA
upper sequence: GLYMA17G01120.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G456690_T01 (Zea mays), 3'ss of exon 2
tactttacattaaaagattgtgtttcttatggggatgctgttgataatgtcaaagtgcaacttttatttggaatcatcatttatttgtctggtaatgcagTGGATGCGTCACATCAGCAGAGACAGTTATGCTGGAGAAGCAAAGTTTGGATGAGTTTCTGAACAATATTAATTCAGGAAAGGCCGTGATTGTGTCTCTT
||| | || | ||| |||| ||| | |||| ||| || | | | | | || | | | ||||||| || ||||| || | |||||||||||||| |||||||||||||| ||||| ||| ||| || | | | || || || | || || || ||||| ||| |
-gtttttccttttttttgtacttttattattcagat-cagttgtgaataagtaacctgatcaagt-tcagtcatgctgactgctttgtctt-tatcttagTGGCTGTATAACATCAGCAGAGACGGTTATGCTGGAGAAACAAAGCTTGAGTGACTTCATTGATCACATAAACTCTGATAAAGCTGTTATTGTATCTGTG
upper sequence: GLYMA17G01120.1 (Glycine max), 3'ss of exon 2
lower sequence: AT4G16440.1 (Arabidopsis thaliana), 3'ss of exon 2
tactttacattaaaagattgtgtttcttatggggatgctgttgataatgtcaaagtgcaacttttatttggaatcatcatttatttgtctggtaatgcagTGGATGCGTCACATCAGCAGAGACAGTTATGCTGGAGAAGCAAAGTTTGGATGAGTTTCTGAACAATATTAATTCAGGAAAGGCCGTGATTGTGTCTCTT
|||| | | | ||| |||| | | ||| || ||| ||||| | | | | || |||||||||| |||||||||| |||||||||||||| ||||||||||| || || |||||||| | ||| ||| |||| |||| ||||||| ||
---------------------gtttgtcctctcatttactttgtctgagtcagttttagagtttagagtgtaatg---gtttatgtatacgattatacagTGGATGCATCACATCAGCTGAGACAGTTATGCTTGAGAAGCAAAGCTTAGACGAGTTTCTCTCTGCTCTTAGCAAAGGCAAGGACGTGGTTGTGTCCGTT
upper sequence: GLYMA17G01120.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv00s0508g00020.t01 (Vitis vinifera), 3'ss of exon 2
----tactttacattaaaagattgtgtttcttatggggatgctgttgataatgtcaaagtgcaacttttatttggaatcatcatttatttgtctggtaatgcagTGGATGCGTCACATCAGCAGAGACAGTTATGCTGGAGAAGCAAAGTTTGGATGAGTTTCTGAACAATATTAATTCAGGAAAGGCCGTGATTGTGTCTCTT
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tctaaaattttggttatgaaaagatttgttaaaggtggcttttcttgggtaagttata--gcaatatggacatcatagaat--ttaacctttttaacgatgcagTGGATGCATAACATCAGCTGAGACTGTGATGCTTGAGAAGCAAAGTATGGATGAGTTTCTCTTTAATATTAACAAAGGGAAGGCAGTCATTGTCTCCCTTMapped 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|192331967|gb|FK024511.1|FK024511EST: GTCAAGTTTGAACCTGTTAAAATTTCGCTTAAGGATTGTTTGGCATGCAG TGGATGCGTCACATCAGCAGAGACAGTTATGCTGGAGAAGCAAAGTTTGGA
genomic: GTCAAGTTTGAACCTGTTAAAATTTCGCTTAAGGATTGTTTGGCATGCAGgtttgtcttt ... ggtaatgcagTGGATGCGTCACATCAGCAGAGACAGTTATGCTGGAGAAGCAAAGTTTGGA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aatgtcaaagtgcaacttttatttggaatcatcatttatttgtctggtaatgcagTGGATGCGTCACATCAGCAGAGACAGTTATGCTGGAGAAGCAAAGTTTGGATGAGTTTCTGAACAATATTAATTCAGGAAAGGCCGTGATTGTGTCTCTT
aatcatcatttattt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tactttacattaaaagattgtgtttcttatggggatgctgttgataatgtcaaagtgcaacttttatttggaatcatcatttatttgtctggtaatgcagTGGATGCGTCACATCAGCAGAGACAGTTATGCTGGAGAAGCAAAGTTTGGATGAGTTTCTGAACAATATTAATTCAGGAAAGGCCGTGATTGTGTCTCTT
- - - - - - - -gattgtg
- - - - - - - - - - - - -cttatgg
- - - - - - - - - - - - - - - - ggatgct
- - - - - - - - - - - - - - - - - - - - - - - - - - -agtgcaa