Sequence
atgc intronic sequence ATGC exonic sequencegtaaacatgacaagtgcctgctagctaccctgaaatttgtgcttaagagtagtattgctttgttttatattatatgcaaacatgtgttgaaagtaaggcattttgatttgacttagatatggtatggtagactaatgcgaagtttgaaagttcatttgttcagGTGCTTGTGAAAGATCTGCTAAGAAAATATCCACAATGGAGTCAGGATTGTATTGCTGTTGTTGGAAATATCAGTAGTAAAAATGTCCAAGAACCCAAGG
Basic information
species | Glycine max |
transcript | GLYMA06G08590.1 |
intron # | 6 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA06G08590.1 (Glycine max), 3'ss of exon 6
lower sequence: LOC_Os01g43630.1 (Oryza sativa), 3'ss of exon 8
gtaaacatgacaagtgcctgctagctaccctgaaatttgtgcttaagagtagtattgctttgttttatattatatgca-aacatgtgttgaaagtaaggcattttgatttgacttagatatggtatggtagactaatgcgaagtttgaaagttcatttgttcagGTGCTTGTGAAAGATCTGCTAAGAAAATATCCACAATGGAGTCAGGATTGTATTGCTGTTGTTGGAAATATCAGTAGTAAAAATGTCCAAGAACCCAAGG
||| || || | ||| ||| || | ||| | | | | | | ||| ||| | ||| | | | | | ||| ||| | | ||| |||| | ||||||||||| | || |||||||| |||||||| || |||||||| || ||||||||||| |||||||| |||||| | || || || || |
------------------------------------------------gtaagtttttttgatagtattttaactgttcatcattcactaaggatgaagtac----attcaactctg----ggtgtctt----tgttcctgagt--aaaaacttaaatgt--agGTCTTGGTGAAAGATCTTTTGAGGAAATATCCTCAATGGAGCCATGATTGTATAGCAGTTGTTGGAAACATCAGTAGCAAAAATATTCAGGAGCCAAAAG
upper sequence: GLYMA06G08590.1 (Glycine max), 3'ss of exon 6
lower sequence: AC198725.4_FGT007 (Zea mays), 3'ss of exon 8
gtaaacatgacaagtgcctgctagctaccctgaaatttgtgcttaagagtagtattgctttgttttatattatatgcaaacatgtgttgaaagtaaggcattttgatttgacttagatatggtatggtagactaatgcgaagtttgaaagttcatttgttcagGTGCTTGTGAAAGATCTGCTAAGAAAATATCCACAATGGAGTCAGGATTGTATTGCTGTTGTTGGAAATATCAGTAGTAAAAATGTCCAAGAACCCAAGG
| ||||| | | | ||| | ||| ||| | | | |||| | | | ||| || | | ||||| | || |||||||| || ||||||||||| |||||||| || |||||||| |||||||||||||||||||| || ||||| |||| || ||||| |
-------------------------------------------------------------------------------gtaagtgtttgtaatgctagttactgacct---ttactcatgatctatt---ctaaca-ggattctga---tttacacatgcagGTCTTGGTAAAAGATCTTCTCAGAAAATATCCTCAATGGAGCCATGATTGTATAGCTGTTGTTGGAAATATCAGCAGCAAAAACATCCAGGAGCCCAAAG
upper sequence: GLYMA06G08590.1 (Glycine max), 3'ss of exon 6
lower sequence: GRMZM2G029077_T01 (Zea mays), 3'ss of exon 6
gtaaacatgacaagtgcctgctagctaccctgaaatttgtgcttaagagtagtattgctttgttttatattatatgcaaacatgtgttgaaagtaaggcattttgatttgacttagatatggtatggtagactaatgcgaagtttgaaagttcatttgttcagGTGCTTGTGAAAGATCTGCTAAGAAAATATCCACAATGGAGTCAGGATTGTATTGCTGTTGTTGGAAATATCAGTAGTAAAAATGTCCAAGAACCCAAGG
| ||| || ||| | | || | | | ||| | | || | | | | |||| ||| |||| || | || | | ||| ||| | | ||||| | ||||||||||| || ||||||||||| ||||||||||| |||||||| || ||||| ||||||||||| || ||||| | || || || || |
----------------------------------gtaagtgttt----gtaatgctagttactgatct-ttactcatgatctagtctagcaggattacgatttacattccacttgtatct----tgatgttttgg------atttaaaaataaa---acgcagGTCTTGGTGAAAGATCTTCTCAGAAAATATCCTCAATGGAGTCATGATTGTATAGCAGTTGTGGGAAATATCAGCAGCAAAAACATTCAGGAGCCAAAAG
upper sequence: GLYMA06G08590.1 (Glycine max), 3'ss of exon 6
lower sequence: Vv04s0008g03880.t01 (Vitis vinifera), 3'ss of exon 6
gtaaacatgacaagtgcctgctagctaccctgaaatttgtgcttaagagtagtattgctttgttttatattatatgcaaacatgtgtt------gaaagtaag--gcattttgatttgacttagatatggtatggtagactaatgcgaagtttgaaagttcatttgttcagGTGCTTGTGAAAGATCTGCTAAGAAAATATCCACAATGGAGTCAGGATTGTATTGCTGTTGTTGGAAATATCAGTAGTAAAAATGTCCAAGAACCCAAGG
|| || | || |||| | | || ||| | | | | | | | ||| | | | | ||| | || | | | ||| ||| || ||| ||| | | | ||| | || | |||| || | |||| | | |||||||||| |||||||||||||| |||||||||||||||||||| ||||| ||||| |||||||| |||||||| || |||||||| || || |||||||
gtgaatttttacagctgtgcctagatgcttggatttttat-tgtgattgaatttgaacattgaaccaaactccaaaaaaatttatgctcttcatgcatagaagtaacatgagcatatgatttaactgttattaatcagattgatac-aagtctgga-gttctctcatgtagGTGCTTGTAAAAGATCTGCTAAGGAAATATCCACAATGGAGTCATGATTGCATTGCAGTTGTTGGGAATATCAGCAGCAAAAATGTTCAGGAGCCCAAGGMapped 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|16348252|gb|BI973847.1|BI973847EST: TTCTCCAGTTTCTTGAGATGGAAAAGGACTATGTTACTTCTGAAGCTCTG GTGCTTGTGAAAGATCTGCTAAGAAAATATCCACAATGGAGTCAGGATTGT
genomic: TTCTCCAGTTTCTTGAGATGGAAAAGGACTATGTTACTTCTGAAGCTCTGgtaaacatga ... atttgttcagGTGCTTGTGAAAGATCTGCTAAGAAAATATCCACAATGGAGTCAGGATTGT
EST:
gi|22524779|gb|BU083590.1|BU083590EST: TTCTCCAGTTTCTTGAGATGGAAAAGGACTATGTTACTTCTGAAGCTCTG GTGCTTGTGAAAGATCTGCTAAGAAAATATCCACAATGGAGTCAGGATTGT
genomic: TTCTCCAGTTTCTTGAGATGGAAAAGGACTATGTTACTTCTGAAGCTCTGgtaaacatga ... atttgttcagGTGCTTGTGAAAGATCTGCTAAGAAAATATCCACAATGGAGTCAGGATTGT
EST:
gi|9820573|gb|BE556083.1|BE556083EST: TTCTCCAGTTTCTTGAGATGGAAAAGGACTATGTTACTTCTGAAGCTCTG GTGCTTGTGAAAGATCTGCTAAGAAAATATCCACAATGGAGTCAGGATTGT
genomic: TTCTCCAGTTTCTTGAGATGGAAAAGGACTATGTTACTTCTGAAGCTCTGgtaaacatga ... atttgttcagGTGCTTGTGAAAGATCTGCTAAGAAAATATCCACAATGGAGTCAGGATTGT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tgacttagatatggtatggtagactaatgcgaagtttgaaagttcatttgttcagGTGCTTGTGAAAGATCTGCTAAGAAAATATCCACAATGGAGTCAGGATTGTATTGCTGTTGTTGGAAATATCAGTAGTAAAAATGTCCAAGAACCCAAGG
gactaat putative branch site (score: 2)
ttcattt putative PPT
tagatat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaaacatgacaagtgcctgctagctaccctgaaatttgtgcttaagagtagtattgctttgttttatattatatgcaaacatgtgttgaaagtaaggcattttgatttgacttagatatggtatggtagactaatgcgaagtttgaaagttcatttgttcagGTGCTTGTGAAAGATCTGCTAAGAAAATATCCACAATGGAGTCAGGATTGTATTGCTGTTGTTGGAAATATCAGTAGTAAAAATGTCCAAGAACCCAAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAC