Sequence
atgc intronic sequence ATGC exonic sequence...attccttttgttcatctttgtttctccactagagaaatttgttacatgtgtccttcttgaaccttttggtgtttcatactgatctttaactaaatttcagGTGCTGGGTAGTGGTTTTGAAGTTATTTCTGTTGGAAAGAAAAAACTTGTTCGTTCAGTTCCAACCGAGTTAAACAAAGACCACAATGAAATTCTAGAAC
Basic information
species | Glycine max |
transcript | GLYMA08G42650.1 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA08G42650.1 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os09g36020.1 (Oryza sativa), 3'ss of exon 4
attccttttgttcatctttgtttctccactagagaaatttgttacatgtgtccttcttgaaccttttggtgtttcatactgatctttaact---aaatttcagGTGCTGGGTAGTGGTTTTGAAGTTATTTCTGTTGGAAAGAAAAAACTTGTTCGTTCAGTTCCAACCGAGTTAAACAAAGACCACAATGAAATTCTAGAAC
|| | | || | ||| | ||| || | || || | |||| || | | | ||| | | |||| || || | |||||| || ||||||||||||||||| ||||||||||| |||||||| ||||| ||||| ||||| || || | || ||||| ||||||| || || || |
gttttacaagattgcattcgaatctatggccaataaaatttt---atttgatgtacttggacagatcgttaattcttctggtcctttgcctgtgaactctcagGTCCTTGGTAGTGGTTTTGAAGTAATTTCTGTTGGGAAGAAAAAGCTTGTGCGTTCTGTTCCTACAGAACTGAATAAAGATCACAATGGGATACTTGAGC
upper sequence: GLYMA08G42650.1 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os11g44790.1 (Oryza sativa), 3'ss of exon 2
attccttttgttcatctttgtttctccactagagaaatttgttacatgtgtccttct-tgaaccttttggtgtttcatactgatctttaactaaatttcagGTGCTGGGTAGTGGTTTTGAAGTTATTTCTGTTGGAAAGAAAAAACTTGTTCGTTCAGTTCCAACCGAGTTAAACAAAGACCACAATGAAATTCTAGAAC
| || ||||| |||| | || | | | | | || | ||| | || || | ||| | || | || | |||||| || ||||||||||||||||| ||||||||||| |||||||| ||||| ||||| ||||| || || | || ||||| ||||||| || || || |
tataattgcattcatgccagttt-tacaagatcgcactcgaatcgattaattcttggacagatctgttaattcttctgatccttcgcttgtgaactctcagGTCCTTGGTAGTGGTTTTGAAGTAATTTCTGTTGGGAAGAAAAAGCTTGTACGTTCTGTTCCTACAGAACTGAATAAAGATCACAATGGGATACTTGAGC
upper sequence: GLYMA08G42650.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G026311_T02 (Zea mays), 3'ss of exon 4
--------attcc-ttttgttcatctttgtttctccactagagaaatttg---ttacatgtgtccttcttgaaccttttggtgtttcat--actgatctttaactaaattt-cagGTGCTGGGTAGTGGTTTTGAAGTTATTTCTGTTGGAAAGAAAAAACTTGTTCGTTCAGTTCCAACCGAGTTAAACAAAGACCACAATGAAATTCTAGAAC
|| ||| | ||| | | | | | ||| |||| | ||||| | | || | | || | |||| || | | | ||| ||||| || ||||||||||||||||| ||||||||||| | || ||| ||||| ||||||||||| ||||| ||||| |||||||||| || || || | |
gtaagactatgaagctttaatgatccatttatatttatcttggaactttggaatcgcatgtatattgtttctatgagtctgtatctcatctgctccttcctttgtggattcgcagGTCCTTGGTAGTGGTTTTGAAGTAATTTCTGTTGGGAGGAGAAAGCTTGTGCGTTCAGTTCCTACCGAATTAAATAAAGACCACAGTGGGATACTTGGGC
upper sequence: GLYMA08G42650.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv19s0090g00070.t01 (Vitis vinifera), 3'ss of exon 4
attccttttgttcatctttgtttctccactagagaaatttgttacatgtgtccttcttgaaccttttggtgtttcatactgatctttaac---taaa---tttcagGTGCTGGGTAGTGGTTTTGAAGTTATTTCTGTTGGAAAGAAAAAACTTGTTCGTTCAGTTCCAACCGAGTTAAACAAAGACCACAATGAAATTCTAGAAC
|| | ||||| | | | || | | | | |||||||| || || | || | | || | || || ||||| |||||||||||||||| || || |||||||||||| ||| |||||| | || || || || ||||| ||||||||||| |||| ||||||||| |
------agtgaacttctttaatataaaagtcaggatgcatctcctaagcagtcttcttgatggttatgatacactgtattaacattcggtgcttgaacctttccagGTATTGGGTAGTGGTTTTGAGGTGATATCTGTTGGAAAGCGAAAGCTTGTTAGGTCTGTCCCTACAGAGTTGAACAAAGACCATAATGCAATTCTAGAGC
upper sequence: GLYMA08G42650.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv19s0090g00110.t01 (Vitis vinifera), 3'ss of exon 1
attccttttgttcatctttgtttctccactagagaaatttgttacatgtgtccttcttgaaccttttggtgtttcatactgatctttaa--ctaaa----tttcagGTGCTGGGTAGTGGTTTTGAAGTTATTTCTGTTGGAAAGAAAAAACTTGTTCGTTCAGTTCCAACCGAGTTAAACAAAGACCACAATGAAATTCTAGAAC
| | ||||| | | || | | | | ||||||| || || | || | | || || | || ||||| |||||||||||||||| || || |||||||||||| ||| |||||| | || || || || ||||| ||||||||||| ||| ||||||||| |
------agcgaacttctttaatataaacgtcaggatgcatctcctaagcagtgttcttgatgtttatgatacactgtattaacattcggtgctcgaacctttccagGTATTGGGTAGTGGTTTTGAGGTGATATCTGTTGGAAAGCGAAAGCTTGTTAGGTCTGTCCCTACAGAGTTGAACAAAGACCATAATTCAATTCTAGAGCMapped 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|19348351|gb|BM892883.1|BM892883EST: GTGAAGTTGTTTCTGAGGATGATTGTCTGCGTGCTATTAAGAAGCTGAAA GTGCTGGGTAGTGGTTTTGAAGTTATTTCTGTTGGA
genomic: GTGAAGTTGTTTCTGAGGATGATTGTCTGCGTGCTATTAAGAAGCTGAAGgtcttgtgct ... taaatttcagGTGCTGGGTAGTGGTTTTGAAGTTATTTCTGTTGGA
EST:
gi|6847785|gb|AW350075.1|AW350075EST: GTGAAGTTGTTTCTGAGGATGATTGTCTGCGTGCTATTAAGAAGCTGAAG GTGCTGGGTAGTGGTTTTGAAGTTATTTCTGTTGGAAAGAAAAAACTTGTT
genomic: GTGAAGTTGTTTCTGAGGATGATTGTCTGCGTGCTATTAAGAAGCTGAAGgtcttgtgct ... taaatttcagGTGCTGGGTAGTGGTTTTGAAGTTATTTCTGTTGGAAAGAAAAAACTTGTT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.atgtgtccttcttgaaccttttggtgtttcatactgatctttaactaaatttcagGTGCTGGGTAGTGGTTTTGAAGTTATTTCTGTTGGAAAGAAAAAACTTGTTCGTTCAGTTCCAACCGAGTTAAACAAAGACCACAATGAAATTCTAGAAC
aactaaa putative branch site (score: 2)
atctttaactaaattt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
attccttttgttcatctttgtttctccactagagaaatttgttacatgtgtccttcttgaaccttttggtgtttcatactgatctttaactaaatttcagGTGCTGGGTAGTGGTTTTGAAGTTATTTCTGTTGGAAAGAAAAAACTTGTTCGTTCAGTTCCAACCGAGTTAAACAAAGACCACAATGAAATTCTAGAAC
- -ccttttg
- - - - - - - - - - - -ctccact
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - catactg