Sequence
atgc intronic sequence ATGC exonic sequence...atggtcctacctttactccgtatataagtaattattagccacccatatattcaaatttctagtttaattgactattcccttttactttggtgtgatgtagTCTTCTTTATGGAGCTGAAGACCCTTCTATTGCTGGAATGGTGTTGGATAGTGCCTTTTCGAACTTATATGATCTCATGATGGAGCTTGTGGATGTTTAT
Basic information
species | Glycine max |
transcript | GLYMA17G00770.1 |
intron # | 6 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA17G00770.1 (Glycine max), 3'ss of exon 6
lower sequence: LOC_Os02g10440.1 (Oryza sativa), 3'ss of exon 5
atggtcctacctttactccgtatataagtaattattagccacccatatattcaaatt---tctagtttaattgact-attcccttttactttggtgtgatgtagTCTTCTTTATGGAGCTGAAGACCCTTCTATTGCTGGAATGGTGTTGGATAGTGCCTTTTCGAACTTATATGATCTCATGATGGAGCTTGTGGATGTTTAT
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----ctttgagttcatgtcatgtataagatgtcttaaatatgtgatctttgcgtaacggatccatcccaattcattcgttgttttgtgaactaatgtaatacagCCTACTCTATGGAGCAGAAGATTCCTCGATTGCTGGAATGGTATTGGATAGTGCTTTCACTAACTTATATGGCTTGATGATGGAGCTTGTGGATGTCTAC
upper sequence: GLYMA17G00770.1 (Glycine max), 3'ss of exon 6
lower sequence: LOC_Os06g40730.1 (Oryza sativa), 3'ss of exon 5
-----atggtcctacctttactccgtatataagtaattattagccacccatatattcaaatttctagtttaattgactattcccttttactttggtgtgatgtagTCTTCTTTATGGAGCTGAAGACCCTTCTATTGCTGGAATGGTGTTGGATAGTGCCTTTTCGAACTTATATGATCTCATGATGGAGCTTGTGGATGTTTAT
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tagaagtacccctgtccataaaatattt-taaatatttaggttctatttatgtattgaattttggtaagttcttcataacttctgtccaaacttttg----acagCCTACTGTATGGAGCAGAAGACCCCTCAATTGCCGGTCTGGTTTTGGACAGTGCTTTCTCTAACCTATATGACTTAATGATGGAGCTTGTAGATGTTTAC
upper sequence: GLYMA17G00770.1 (Glycine max), 3'ss of exon 6
lower sequence: GRMZM2G092895_T01 (Zea mays), 3'ss of exon 5
atggtcctacctttactccgtatataagtaattattagccacccatatattcaaatttctagtttaattgactattcccttttactttg-gtgtgatgtagTCTTCTTTATGGAGCTGAAGACCCTTCTATTGCTGGAATGGTGTTGGATAGTGCCTTTTCGAACTTATATGATCTCATGATGGAGCTTGTGGATGTTTAT
||| || | || | | | || || | | | | | || | | ||| || || | ||| || || || || ||||| || |||||||| |||||||| || |||||||| ||||| |||||||||| || | ||||||||||| | |||||||||||||| || |||||
-cggtacttgcatttaacgctgcaaaatatcttgatttaaattattcttgatatatgtgcattttgatatttcatgacaatttgtgttatgtctgctgcagTCTGCTATATGGAGCAGAAGACCCCTCAATTGCTGGCATGGTTCTGGATAGTGCTTTCGCTAACTTATATGACTTAATGATGGAGCTTGTAGAAGTTTAC
upper sequence: GLYMA17G00770.1 (Glycine max), 3'ss of exon 6
lower sequence: GRMZM2G081642_T04 (Zea mays), 3'ss of exon 5
--atggtcctacctttactccgtatataagtaattattagccacccatatattcaaatttctagtttaattgactattcccttttactttggtgtga-tgtagTCTTCTTTATGGAGCTGAAGACCCTTCTATTGCTGGAATGGTGTTGGATAGTGCCTTTTCGAACTTATATGATCTCATGATGGAGCTTGTGGATGTTTAT
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ccgctttaaaaaccatggtcaagcttgaaatatctcatcaccacttgatggctgtcccctttaattctttacaatatt---ttgtatacaaatgtaaatacagCCTACTCTATGGAGCAGAGGACCCTTCTATTGGTGGCATGATATTGGATAGTGCCTTCACTAACCTGTATGACTTGATGATGGAACTTGTTGACGTTTAC
upper sequence: GLYMA17G00770.1 (Glycine max), 3'ss of exon 6
lower sequence: AT4G17150.2 (Arabidopsis thaliana), 3'ss of exon 5
------------------------------------------------------------atggtcctacctttactccgtatataagtaatt--attagccacccatatattcaaatttc---tagtttaattgactattcccttttactttggtgtgatgt--agTCTTCTTTATGGAGCTGAAGACCCTTCTATTGCTGGAATGGTGTTGGATAGTGCCTTTTCGAACTTATATGATCTCATGATGGAGCTTGTGGATGTTTAT
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gttacttcttgagctacttttcagtcacacttaaaagtagtattagtagttgtgttgactatagattcaccagctttctaaaggtctatgatctgaaaagtgtgtcaactctccacatttcatcttgttctctccatcatttgatgaagcgggaatataatgtgcagCCTTCTCTATGGAGCAGAAGATCCTTCAATTGCTGGAATGGTCCTAGACAGTGCATTTTCAAACTTATTTGATCTGATGATGGAACTAGTGGATGTCTACMapped 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|58021185|gb|CX707927.1|CX707927EST: CAAATATCTCGTATAGGTCTTTGGGGACGATCTATGGGTGCTGTTACTAG TCTTCTTTATGGAGCTGAAGACCCTTCTATTGCTGGAATGGTGTTGGATAG
genomic: CAAATATCTCGTATAGGTCTTTGGGGACGATCTATGGGTGCTGTTACTAGgtattacatc ... tgtgatgtagTCTTCTTTATGGAGCTGAAGACCCTTCTATTGCTGGAATGGTGTTGGATAG
EST:
gi|58014297|gb|CX701039.1|CX701039EST: GGGGACGATCTATGGGTGCTGTTACTAG TCTTCTTTATGGAGCTGAAGACCCTTCTATTGCTGGAATGGTGTTGGATAG
genomic: GGGGACGATCTATGGGTGCTGTTACTAGgtattacatc ... tgtgatgtagTCTTCTTTATGGAGCTGAAGACCCTTCTATTGCTGGAATGGTGTTGGATAG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tatattcaaatttctagtttaattgactattcccttttactttggtgtgatgtagTCTTCTTTATGGAGCTGAAGACCCTTCTATTGCTGGAATGGTGTTGGATAGTGCCTTTTCGAACTTATATGATCTCATGATGGAGCTTGTGGATGTTTAT
aattgac putative branch site (score: 3)
aaatttctagtttaat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
atggtcctacctttactccgtatataagtaattattagccacccatatattcaaatttctagtttaattgactattcccttttactttggtgtgatgtagTCTTCTTTATGGAGCTGAAGACCCTTCTATTGCTGGAATGGTGTTGGATAGTGCCTTTTCGAACTTATATGATCTCATGATGGAGCTTGTGGATGTTTAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCTT
- - -cctacct
- - - - - - - - - - - - - - - - - - - -cacccat