Sequence
atgc intronic sequence ATGC exonic sequence...ggattttgatctagataaaattatataggtgtactggcagctgactcattgaaattgaatctttttcagaagctaatggttttactgattattctttgcaGACCTCGAAACAAATGAGTGTTTGGAAAACAATGGTGGTTGTTGGCAGGACAAATCTTCTAACATTACTGCATGCAG
Basic information
species | Glycine max |
transcript | GLYMA18G44580.1 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA18G44580.1 (Glycine max), 3'ss of exon 5
lower sequence: LOC_Os11g02464.1 (Oryza sativa), 3'ss of exon 5
--------------------ggattttgatctagataa--aattat-ataggtgtactggcagctgactcattgaaattgaatctt--tttcagaagctaatggttttactgattattctttgcaGACCTCGAAACAAATGAGTGTTTGGAAAACAATGGTGGTTGTTGGCAGGACAAATCTTCTAACATTACTGCATGCAG-
| ||| |||| | | | || ||| | |||| || | ||| ||| ||| || | | | || | | | ||| ||| | ||||||||||||| ||||| ||||||||||| |||||||| ||||| || ||||||| |||||||||
gttggtgcattaatttcaataggtttctatctgtttgctcattcatgataaaaatttatacagcaagcttaacttgcttgggccttgcttttagtatttgttcattcatgttacttcgaattgtagATATACAAACAAATGAGTGCTTGGAGAACAATGGTGGCTGTTGGCAAGACAAGGCTGCTAACATCTCTGCATGCAAG
upper sequence: GLYMA18G44580.1 (Glycine max), 3'ss of exon 5
lower sequence: LOC_Os12g02390.1 (Oryza sativa), 3'ss of exon 5
--------------------ggattttgatctagata--aaattat-ataggtgtactggcagctgactcattgaaattgaatctt--tttcagaagctaatggtt--ttactgattattctt-----tgcaGACCTCGAAACAAATGAGTGTTTGGAAAACAATGGTGGTTGTTGGCAGGACAAATCTTCTAACATTACTGCATGCAG-
|||||| |||| | | | || ||| | |||| || | ||| ||| ||| || | | | || | | | || | ||| || ||| | ||||||||||||| ||||| ||||||||||| |||||||| ||||| || ||||||| |||||||||
gttggtgcattaatttcaatagatttttatctgtttgctcattcatgataaaaatttatacagcaagcttaacttgcttgggccttgcttttagtatttgttcattcatgattcatgttacttcgaactgtagATATACAAACAAATGAGTGCTTGGAGAACAATGGTGGCTGTTGGCAAGACAAGGCTGCTAACATCTCTGCATGCAAG
upper sequence: GLYMA18G44580.1 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM2G389362_T01 (Zea mays), 3'ss of exon 6
----ggattttgatctagataaaattatataggtgtactggc------agctgactca---ttgaaattgaatctttttcagaagctaatggttttactgattattctttg----caGACCTCGAAACAAATGAGTGTTTGGAAAACAATGGTGGTTGTTGGCAGGACAAATCTTCTAACATTACTGCATGCAG-
| | || || | ||| |||| | || |||| | || || | || || || | || | | | | || | ||| | |||| ||| | ||||||||||||| | || ||||||||||| |||||||| || || || ||||||| ||||||||||
gttggtacatttatttccctaat-ttattcatgttcactgcttacataatctagcttatgcttccaagtgtaatttgcatgtagcatgctcttaatattcattttattttgatcttagATATACAAACAAATGAGTGCCTAGAGAACAATGGTGGCTGTTGGCAAGATAAGGCTGCTAACATCACTGCATGCAAG
upper sequence: GLYMA18G44580.1 (Glycine max), 3'ss of exon 5
lower sequence: AT3G52850.1 (Arabidopsis thaliana), 3'ss of exon 5
------------------------------------------------------------------ggattttgatctagataaaattatataggtg-tactggcagctgactcattgaaattgaatctttttc-agaagctaatggtttt---ac-tgattat--tctttgcaGACCTCGAAACAAATGAGTGTTTGGAAAACAATGGTGGTTGTTGGCAGGACAAATCTTCTAACATTACTGCATGCAG-
|| | || | | ||| || || | | || | | | | || || | | ||| || ||||| || || || | | |||||||| | ||||| ||||| |||||||||||||| ||||| || ||||| |||||| || | |||||||||||||||||
gtactattatccacgacatttgcaactctattttttttaacagaaaccacagttctcttgataggccaatatatattttca-aaacttgcattagagctatccttaattctttatctattgttttatatcatgggagagaaggatagttttcagacatgcttctgatttttgcagATTTGGAAACTAATGAATGTTTGGAAAACAACGGTGGATGCTGGCAAGACAAAGCTGCCAACATTACTGCATGCAGG
upper sequence: GLYMA18G44580.1 (Glycine max), 3'ss of exon 5
lower sequence: Vv08s0058g01360.t01 (Vitis vinifera), 3'ss of exon 5
ggattttgatctagataa-aattatataggtgtactggcagctgactcattgaaattgaatctttttcagaagctaa-tggttttactgattattctttgcaGACCTCGAAACAAATGAGTGTTTGGAAAACAATGGTGGTTGTTGGCAGGACAAATCTTCTAACATTACTGCATGCAG-
|| || || || || || || | ||| | ||| | | | | |||| | | | || | | | | |||| | |||| | || |||||||||||||||||||| |||||||| || |||||||| || || |||| |||||||||||||
-tatattatattatttaggaaataaattgtggtat--gaagcaaatgagtacacacccttgtggaatcagtattcatcttcttctgttaactgttctctacagAGGTAGAGACAAATGAGTGTTTGGAAAATAATGGTGGATGCTGGCAGGATAAGGCTGCTAATATTACTGCATGCAAGMapped 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|20497891|gb|BQ272821.1|BQ272821EST: TCTGTTCAGGCTTCCTAGAGACCACTGAACCATCAATTTGCTTAACTTCA GACCTCGAAACAAATGAGTGTTTGGAAAACAATGGTGGTTGTTGGCAGGAC
genomic: TCTGTTCAGGCTTCCTAGAGACCACTGAACCATCAATTTGCTTAACTTCAggtcattttt ... attctttgcaGACCTCGAAACAAATGAGTGTTTGGAAAACAATGGTGGTTGTTGGCAGGAC
EST:
gi|13478328|gb|BG507848.1|BG507848EST: TCTGTTCAGGCTTCCTAGAGACCACTGAACCATCAATTTGCTTAACTTCA GACCTCGAAACAAATGAGTGTTTGGAAAACAATGGTGGTTGTTGGCAGGAC
genomic: TCTGTTCAGGCTTCCTAGAGACCACTGAACCATCAATTTGCTTAACTTCAggtcattttt ... attctttgcaGACCTCGAAACAAATGAGTGTTTGGAAAACAATGGTGGTTGTTGGCAGGAC
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tcattgaaattgaatctttttcagaagctaatggttttactgattattctttgcaGACCTCGAAACAAATGAGTGTTTGGAAAACAATGGTGGTTGTTGGCAGGACAAATCTTCTAACATTACTGCATGCAG
tactgat putative branch site (score: 2)
ttattcttt CT-rich tract
aaattgaatcttttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ggattttgatctagataaaattatataggtgtactggcagctgactcattgaaattgaatctttttcagaagctaatggttttactgattattctttgcaGACCTCGAAACAAATGAGTGTTTGGAAAACAATGGTGGTTGTTGGCAGGACAAATCTTCTAACATTACTGCATGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG
- - - - - - agataaaa
- - - - - - - - - - - - - - - - - - -cagctga
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gctaatg