Sequence
atgc intronic sequence ATGC exonic sequence...tggcttaacctaactgaaagatgatacaatttgtagcaaatatacctgtgatgccatttgttactatttggttggctcaaatgcatgttactcatgtcagGTGAACCCACACACTCATCAGCTGAAACTATGTGATTTTGGGAGTGCAAAAGTGTTG
Basic information
species | Glycine max |
transcript | GLYMA16G00400.1 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA16G00400.1 (Glycine max), 3'ss of exon 5
lower sequence: LOC_Os03g62500.1 (Oryza sativa), 3'ss of exon 6
tggcttaacctaactgaaagatgatacaatttgtagcaaatatacctgtgatgccatttgttactatttggttggctcaaatgcatgttact---catgtcagGTGAACCCACACACTCATCAGCTGAAACTATGTGATTTTGGGAGTGCAAAAGTGTTG
||| | || | | | | | ||| || || ||| || |||| | | || | || || || |||| |||||||| || || ||||| ||| ||||||||||||| ||||||||||| |||
--acttcaattatttattttaaaaccgtgatcat-gcatgtacttacagactgaaattcactaagttttgatggtactaataaggtcttccttcgcactgtagGTTAACCCACATACACACCAGCTCAAAATATGTGATTTTGGCAGTGCAAAAGTTTTG
upper sequence: GLYMA16G00400.1 (Glycine max), 3'ss of exon 5
lower sequence: AT1G09840.6 (Arabidopsis thaliana), 3'ss of exon 6
tggcttaa----cctaactgaaagatgatacaatttgtagcaaatatacctgtgatgccatttgttactatttggttggctcaaatgcatgttactcatgtcagGTGAACCCACACACTCATCAGCTGAAACTATGTGATTTTGGGAGTGCAAAAGTGTTG
|||||| |||||| | | || | | | ||| | | || ||| | || || | ||||| | || ||||||||||||||||| |||||||| ||| |||||||||| ||||||||||||||||||
-agcttaaaaattctaactagttagaattgctatctaaaaagttgttcggtgttaatttaaatgcatttatatatctgacttta-cagatgttgtt-gtg-cagGTGAACCCACACACGCATCAGCTAAAAATATGTGATTTCGGGAGTGCAAAAGTGTTG
upper sequence: GLYMA16G00400.1 (Glycine max), 3'ss of exon 5
lower sequence: AT1G57870.3 (Arabidopsis thaliana), 3'ss of exon 7
tggcttaacctaactgaaagatgatacaatttgt----agcaaatatacctgtgatgccatttgttactatttggttggctcaaatgcatgt-tactcatgt-cagGTGAACCCACACACTCATCAGCTGAAACTATGTGATTTTGGGAGTGCAAAAGTGTTG
| | || ||| || || ||||||| | ||||| | | || | ||| | | ||| || | | || | | | |||| |||||||| |||||||| |||||||||||| | |||||||||||||||||||||||||||
------accatacctgcaattgactagaatttgtcataaacaaatgttgccttgtttttattaaacaatcttttatttttttctttacacctattgtgatgtgcagGTGAATCCACACACACATCAGCTGAAAATTTGTGATTTTGGGAGTGCAAAAGTGTTG
upper sequence: GLYMA16G00400.1 (Glycine max), 3'ss of exon 5
lower sequence: Vv12s0035g01060.t01 (Vitis vinifera), 3'ss of exon 5
-------tggcttaac---ctaactgaaagatgatacaatttgtagcaaatatacctgtgatgccatttgttactatttggttggctcaaatgcatgttactcatgtcagGTGAACCCACACACTCATCAGCTGAAACTATGTGATTTTGGGAGTGCAAAAGTGTTG
| |||| | |||||| | | ||| | | || || | | ||| || | || || | | ||| | |||| ||||| |||||||||||||||||| |||||||||||||| ||||||||||||||||| ||||| |||
tttggacagacttatcaggctaactccatggtga--cgacttttaaattttgatcttgttatcttactttgtaagactgatttg--ttaaat---tgttatgt---tcagGTGAACCCACACACGCATCAGCTGAAACTTTGTGATTTTGGGAGTGCGAAAGTTTTGMapped 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|26047783|gb|CA784461.1|CA784461EST: ATAACTGCATTGGTATATGTCATCGTGACATCAAACCTCAGAACCTACTT GTGAACCCACACACTCATCAGCTGAAACTATGTGATTTTGGGAGTGCAAAA
genomic: ATAACTGCATTGGTATATGTCATCGTGACATCAAACCTCAGAACCTACTTgtaagatatt ... ctcatgtcagGTGAACCCACACACTCATCAGCTGAAACTATGTGATTTTGGGAGTGCAAAA
EST:
gi|26048721|gb|CA785174.1|CA785174EST: ATAACTGCATTGGTATATGGCATCGTGACATCAAACCTCAAAACCTACTT GTGAACCCACACACTCATCAACTGAAACTATGTGATTTTGGG
genomic: ATAACTGCATTGGTATATGTCATCGTGACATCAAACCTCAGAACCTACTTgtaagatatt ... ctcatgtcagGTGAACCCACACACTCATCAGCTGAAACTATGTGATTTTGGG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ctgtgatgccatttgttactatttggttggctcaaatgcatgttactcatgtcagGTGAACCCACACACTCATCAGCTGAAACTATGTGATTTTGGGAGTGCAAAAGTGTTG
atttgttactattt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tggcttaacctaactgaaagatgatacaatttgtagcaaatatacctgtgatgccatttgttactatttggttggctcaaatgcatgttactcatgtcagGTGAACCCACACACTCATCAGCTGAAACTATGTGATTTTGGGAGTGCAAAAGTGTTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGA