Sequence
atgc intronic sequence ATGC exonic sequence...gtaaaaattattgcattcatgaagtattctgttttcccagtgaactaatggaatgctaggcatgaattaactaacatgttttatcctatttgtgctttagATGGTAAAGAGACCTCTAACAGTGATGCTCCTGAGAACAATCCTCAGTATACTACGGTTTATGTGGGTAACCTTGCTCCGGAG
Basic information
species | Glycine max |
transcript | GLYMA16G01230.1 |
intron # | 9 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA16G01230.1 (Glycine max), 3'ss of exon 9
lower sequence: AT1G17370.2 (Arabidopsis thaliana), 3'ss of exon 9
-------gtaaa---aattattgcat-tcatgaagtattctgttttcccagtgaactaatggaatgctaggcatgaattaa----ctaac------atgttt------tatcctatttgtgcttt----agATGGTAAAGAGACCTCTAACAGTGATGCTCCTGAGAACAATCCTCAGTATACTACGGTTTATGTGGGTAACCTTGCTCCGGAG
||| || |||| | | ||||||| || || | ||| || | || || || || | | |||| |||||| | | ||||||| | | ||||||||||| || |||| |||| ||||||||||||||| ||||||| || || ||||| || ||||| |||||||| |||
gtctcgggtatgtttaactattacctatcatgaaatag---aaaatcaaatggaaatagagaaaagcctcaaataaacttaattcttaaccctttgatgtttatacattggcttatttgttcctgcagagGATGGTAAAGATACTACTAATGGTGAAGCTCCTGAGAACAATGCTCAGTACACAACTGTTTACGTCGGTAATCTTGCTCCAGAG
upper sequence: GLYMA16G01230.1 (Glycine max), 3'ss of exon 9
lower sequence: AT1G17370.1 (Arabidopsis thaliana), 3'ss of exon 9
gtaaa---aattattgcat-tcatgaagtattctgttttcccagtgaactaatggaatgctaggcatgaattaa----ctaac------atgttt------tatcctatttgtgcttt----agATGGTAAAGAGACCTCTAACAGTGATGCTCCTGAGAACAATCCTCAGTATACTACGGTTTATGTGGGTAACCTTGCTCCGGAG
||| || |||| | | ||||||| || || | ||| || | || || || || | | |||| |||||| | | ||||||| | | ||||||||||| || |||| |||| ||||||||||||||| ||||||| || || ||||| || ||||| |||||||| |||
gtatgtttaactattacctatcatgaaatag---aaaatcaaatggaaatagagaaaagcctcaaataaacttaattcttaaccctttgatgtttatacattggcttatttgttcctgcagAGGATGGTAAAGATACTACTAATGGTGAAGCTCCTGAGAACAATGCTCAGTACACAACTGTTTACGTCGGTAATCTTGCTCCAGAG
upper sequence: GLYMA16G01230.1 (Glycine max), 3'ss of exon 9
lower sequence: Vv09s0002g00880.t01 (Vitis vinifera), 3'ss of exon 9
gtaaaaattattgcattcatgaagtattctgttttcccagtgaactaatgga----atgctaggcatgaattaactaacatgttttatcctatttgtgctttagATGGTAAAGAGACCTCTAACAGTGATGCTCCTGAGAACAATCCTCAGTATACTACGGTTTATGTGGGTAACCTTGCTCCGGAG
|| || || | | | || ||| | | | | | | | || ||| ||| || | | || | | | || | |||||| ||||||||||||||| | | | ||| |||||||| ||||| ||||||||||| || ||||||||||| || |||||||| |||
tcaaggatgcttttgtac-taaatcattgtctcctttggattatatgctagagattatgatagtgataagaaaccttatgtttgttgcattccttgtgcagAAGATGGTAAAGAGACAGCAACTAATGAGGCTCCTGACAACAACCCTCAGTATACAACTGTTTATGTGGGCAATCTTGCTCCAGAGMapped 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|26058275|gb|CA801189.1|CA801189EST: GCAAAACTCAGATGCAAAAAGTGTGGTGGAACTAACGTATGGCTCATCTG ATGGTAAAGAGACCTCTAACAGTGATGCTCCTGAGAACAATCCTCAGTATA
genomic: GCAAAACTCAGATGCAAAAAGTGTGGTGGAACTAACGTATGGCTCATCTGgtcagtacac ... tgtgctttagATGGTAAAGAGACCTCTAACAGTGATGCTCCTGAGAACAATCCTCAGTATA
EST:
gi|6951590|gb|AW423658.1|AW423658EST: GCAAAACTCAGATGCAAAAAGTGTGGTGGAACTAACGTATGGCTCATCTG ATGGTAAAGAGACCTCTAACAGTGATGCTCCTGAGAACAATCCTCAGTATA
genomic: GCAAAACTCAGATGCAAAAAGTGTGGTGGAACTAACGTATGGCTCATCTGgtcagtacac ... tgtgctttagATGGTAAAGAGACCTCTAACAGTGATGCTCCTGAGAACAATCCTCAGTATA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.taatggaatgctaggcatgaattaactaacatgttttatcctatttgtgctttagATGGTAAAGAGACCTCTAACAGTGATGCTCCTGAGAACAATCCTCAGTATACTACGGTTTATGTGGGTAACCTTGCTCCGGAG
aactaac putative branch site (score: 1)
tcctattt putative PPT
aattaactaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaaaaattattgcattcatgaagtattctgttttcccagtgaactaatggaatgctaggcatgaattaactaacatgttttatcctatttgtgctttagATGGTAAAGAGACCTCTAACAGTGATGCTCCTGAGAACAATCCTCAGTATACTACGGTTTATGTGGGTAACCTTGCTCCGGAG
- - - - - - gcattca
- - - - - - - - - - - - - ttctgtt
- - - - - - - - - - - - - - - - -ttcccag
- - - - - - - - - - - - - - - - - - - - - - - - - gaatgct
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gcatgaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -actaaca