Sequence
atgc intronic sequence ATGC exonic sequencegtttgcccttttcaactgtaaactaataatgggcatgagtctatagctagtcccttcaagaactggaaatctattatatctgatatcaaataatgctctgctctgcagGTTATTTTTAATTTTGGTCCAAAAGTGTCCATATTCACATTTTATTCAGACGAAGATAAGTTTCTGTTCATGTGAATTGTAGTGTCGAAGCAACTTGATG
Basic information
species | Glycine max |
transcript | GLYMA15G05410.4 |
intron # | 8 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA15G05410.4 (Glycine max), 3'ss of exon 8
lower sequence: LOC_Os03g49520.2 (Oryza sativa), 3'ss of exon 8
-----------------------------gtttgcccttttcaactgtaaactaataatgggcatgagtctatagctagtcccttcaagaactggaa----atctattata-tctgatatcaaataat---gctctgctctgcagGTTATTTTTAATTTTGGTCCAAAAGTGTCCATATTCACATTTTATTCAGACGAAGATAAGTTTCTGTTCATGTGAATTGTAGTGTCGAAGCAACTTGATG
|| | | || | | | | | | | | | | | ||| | | | || ||| || ||| ||| || | | | || |||||||||||||||| | |||||||||||| |||||||| ||| || | | |||||| ||||||| | || ||| | ||| | | | |
gtcgctttacttctttgcatcattctgcacctttttttatccatgaatggggtccctttttgtttccttttgttgtgccactttgcaatatttttatctgtatttatcttactcttttatgaactggtcttattgtgtgctgcagGTTATTTTTATTCCTGGTCCAAAAGTATCCATATTGACAATTAAATTGAGGGAAGATGCGTTTCTGATTGTGCAAATCTTGATGTTTGATGTTCATAGGG
upper sequence: GLYMA15G05410.4 (Glycine max), 3'ss of exon 8
lower sequence: GRMZM2G102475_T02 (Zea mays), 3'ss of exon 8
------------------------gtttgccct--tttcaactgtaaactaataatgggcatgagtctatagcta--gtcccttcaagaact------ggaaatctattatatc---tgat--atcaaataatg-ctctgctctgcagGTTATTTTTAATTTTGGTCCAAAAGTGTCCATATTCACATTTTATTCAGACGAAGATAAGTTTCTGTTCATGTGAATTGTAGTGTCGAAGCAACTTGATG
|| | | || || ||||| ||| ||| ||| | || | |||| | | || |||| | | || |||| ||| || | || || ||||||||||||||||| || ||||||||||||||||||||| ||| || | | ||||||| || ||
gtaactttgctgctttgcatcaatcttcactttaacttagacccaaaacttggaatcctcattt-tcttcacttaaagctgtttcacatgtttatgtagtaattctactctctcgtttgatggatctgttattttctgtgttctgcagGTTATTTTTATTTCTGGTCCAAAAGTGTCCATATTGACAATTAAATTGAGGGAAGATACATTCTAATT--------------------------------
upper sequence: GLYMA15G05410.4 (Glycine max), 3'ss of exon 8
lower sequence: GRMZM5G810275_T02 (Zea mays), 3'ss of exon 8
---------------------gtttgcccttttcaactgtaaactaataatggg--catgagtctat-------agctagtcccttca--agaactggaaatctatta---tatctgat--atcaaataatg-ctctgctctgcagGTTATTTTTAATTTTGGTCCAAAAGTGTCCATATTCACATTTTATTCAGACGAAGATAAGTTTCTGTTCATGTGAATTGTAGTGTCGAAGCAAC-TTGATG-
|| | |||| | | | | || | ||| | | | | | |||| | || | | | || |||| || | | ||| ||| || | || || ||||||||||||||||| || ||||||||||||||||||||| ||| || | | ||||||| || || | ||| | | | ||| | | | || ||
gtagctttgctgctttgcatcattcttcattttgagttagacccaaaaattggaacccccattttctttacataagctgtttcccatgtttgtgcagtaattctactatcttgtttgaatgatctgttattttctgtgttctgcagGTTATTTTTATTTCTGGTCCAAAAGTGTCCATATTGACAATTAAATTGAGGGAAGATACATT-CTAATTATGCAGACT-TGATGTTTGATAACCATTAGTGT
upper sequence: GLYMA15G05410.4 (Glycine max), 3'ss of exon 8
lower sequence: GRMZM2G102475_T01 (Zea mays), 3'ss of exon 8
------------------------gtttgccct--tttcaactgtaaactaataatgggcatgagtctatagcta--gtcccttcaagaact------ggaaatctattat---atctgat--atcaaataatg-ctctgctctgcagGTTATTTTTAATTTTGGTCCAAAAGTGTCCATATTCACATTTTATTCAGACGAAGATAAGTTTCTGTT-CATGT-GAATTGTAGTGTCGAAGCAACTTGATG
|| | | || || ||||| ||| ||| ||| | || | |||| | | || |||| | | | |||| ||| || | || || ||||||||||||||||| || ||||||||||||||||||||| ||| || | | ||||||| || || ||| || || || | | | | | |
gtaactttgctgctttgcatcaatcttcactttaacttagacccaaaacttggaatcctcattt-tcttcacttaaagctgtttcacatgtttatgtagtaattctactctctcgtttgatggatctgttattttctgtgttctgcagGTTATTTTTATTTCTGGTCCAAAAGTGTCCATATTGACAATTAAATTGAGGGAAGATACATTCTAATTGTATGCAGACCTGATGTTTGATAACTATTAGT--
upper sequence: GLYMA15G05410.4 (Glycine max), 3'ss of exon 8
lower sequence: Vv12s0055g00360.t01 (Vitis vinifera), 3'ss of exon 9
gtttgcccttttcaactgtaaactaataatgggcatgagtctatagctagtcccttcaagaactggaaatctattatatctgatatcaaataatgctctgctctgcagGTTATTTTTAATTTTGGTCCAAAAGTGTCCATATTCACA-TTTTATTCAGACGAAGATAAGTTTCTGTTCATGTGAATTGTAGTGTCGAAGCAACT-TGATG---------------------------
||||||||||||||||||||||| ||||||| ||||||||||||||||||||||||||| || ||||| ||||||||| |||
----------------------------------------------------------------------------------------------------------------------------gtccaaaagtgtccatattcacaattttattgagacgaagataagtttctgttcatgtgcat---agtgttgaagcaactgtgaccatttcctgcttctttgcagGATCTTAGMapped 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|207811816|gb|GD783065.1|GD783065EST: CTGTTTCTTCAGTGGAGTGAGCATCGTAAAAGACTAAGCAATTTTATAAG GTTATTTTTAATTTTGGTCCAAAAGTGTCCATATTCACATTTTATTCAGAC
genomic: CTGTTTCTTCAGTGGACTGAGCATCATAAAAGACTAAGCAATTTTATAAGgtttgccctt ... tgctctgcagGTTATTTTTAATTTTGGTCCAAAAGTGTCCATATTCACATTTTATTCAGAC
EST:
gi|8669745|gb|BE190852.1|BE190852EST: CTGTTTCTTCAGTGGACTGAGCATCATAAAAGACTAAGCAATTTTATAAG GTTATTTTTAATTTTGGTCCAAAAGTGTCCATATTCACATTTTATTCAGAC
genomic: CTGTTTCTTCAGTGGACTGAGCATCATAAAAGACTAAGCAATTTTATAAGgtttgccctt ... tgctctgcagGTTATTTTTAATTTTGGTCCAAAAGTGTCCATATTCACATTTTATTCAGAC
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.cttcaagaactggaaatctattatatctgatatcaaataatgctctgctctgcagGTTATTTTTAATTTTGGTCCAAAAGTGTCCATATTCACATTTTATTCAGACGAAGATAAGTTTCTGTTCATGTGAATTGTAGTGTCGAAGCAACTTGATG
atctgat putative branch site (score: 4)
ctctgctct putative PPT
aaatctattatatctg 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtttgcccttttcaactgtaaactaataatgggcatgagtctatagctagtcccttcaagaactggaaatctattatatctgatatcaaataatgctctgctctgcagGTTATTTTTAATTTTGGTCCAAAAGTGTCCATATTCACATTTTATTCAGACGAAGATAAGTTTCTGTTCATGTGAATTGTAGTGTCGAAGCAACTTGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA