Sequence
atgc intronic sequence ATGC exonic sequencegtttcttttctaatttaattggataagttaatactttcttgttgactatagattttaatgttgttgttatataattacagTCCAAGAGCTTAAATATCAGTCGGGATGTTTCTGGTGAGGGTGTTCAGCAGGCATTATTGAAAATGCTTGAAGGAACT
Basic information
species | Glycine max |
transcript | GLYMA16G33080.1 |
intron # | 7 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA16G33080.1 (Glycine max), 3'ss of exon 7
lower sequence: GRMZM2G050186_T03 (Zea mays), 3'ss of exon 5
gtttcttttctaatttaattggataagttaatactttcttgttgactatagattttaatgttgttgttatataat-tacagTCCAAGAGCTTAAATATCAGTCGGGATGTTTCTGGTGAGGGTGTTCAGCAGGCATTATTGAAAATGCTTGAAGGAACT
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-----gtatgtcatatcaatctttggcttggattttccctcctgg-tgtgggcgttgattagtttgtgatttggcatgcagGCTGAAAGTCTTAACATTAGCAGAGACGTATCTGGTGAAGGTGTTCAGCAGGCATTGCTGAAAATGCTGGAAGGCACG
upper sequence: GLYMA16G33080.1 (Glycine max), 3'ss of exon 7
lower sequence: GRMZM2G101791_T01 (Zea mays), 3'ss of exon 6
gtttcttttctaatttaattggataagttaatactttcttgttgactatagattttaatgttgttgttatataat-tacagTCCAAGAGCTTAAATATCAGTCGGGATGTTTCTGGTGAGGGTGTTCAGCAGGCATTATTGAAAATGCTTGAAGGAACT
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-------gtatgacatcaatctttggcttgaattttccctcctgg-tgtggacattcattagtttgtgatctggcatgcagGCTGAAAGTCTTAACATCAGCAGAGACGTATCTGGTGAAGGTGTTCAGCAGGCATTGCTGAAAATGCTGGAAGGCACG
upper sequence: GLYMA16G33080.1 (Glycine max), 3'ss of exon 7
lower sequence: Vv18s0089g01240.t01 (Vitis vinifera), 3'ss of exon 6
----------------gtttcttttctaatttaattggataagttaatactttcttgttgactatagattttaatgttgt-tgttatataattacagTCCAAGAGCTTAAATATCAGTCGGGATGTTTCTGGTGAGGGTGTTCAGCAGGCATTATTGAAAATGCTTGAAGGAACT
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gttccacagttttccagcttatttatttattt--ttatttaaatttaggtgtctttgtaaaaccaaaagtgcacttaaatgtggaaaccttttgcagGCTGAGAGCTTAAACCTTAGCAGAGATGTTTCTGGTGAGGGTGTTCAGCAAGCATTACTGAAAATGCTGGAAGGAACT
upper sequence: GLYMA16G33080.1 (Glycine max), 3'ss of exon 7
lower sequence: PP1S163_100V6.1 (Physcomitrella patens), 3'ss of exon 6
---------------gtttcttttctaatttaattggataagttaatac------tttcttgttgactatagatt-ttaatgttgt-tgttatataattacagTCCAAGAGCTTAAATATCAGTCGGGATGTTTCTGGTGAGGGTGTTCAGCAGGCATTATTGAAAATGCTTGAAGGAACT
||| ||| || || | | || |||| || |||| | ||| | || |||| | | | || || || ||| | ||| | || || || ||||||| |||||||| || |||||||||||| | ||||| ||||| |||||||||
gagtccctgttcttagttacttctcaggagtag--gagcacattgatacctcctcttccttgctttctaaaaatcattaacaatatgtatttgattgtt-cagGCGGAGAATATGAACATTAGCAGGGATGTATCTGGTGAAGGAGTTCAGCAGGCACTTTTGAAGATGCTGGAAGGAACT
upper sequence: GLYMA16G33080.1 (Glycine max), 3'ss of exon 7
lower sequence: PP1S98_222V6.1 (Physcomitrella patens), 3'ss of exon 7
------------gtttcttttctaa-tttaattggataagttaatactttcttgttgactatagatt------ttaatgttg----ttgttatataattacagTCCAAGAGCTTAAATATCAGTCGGGATGTTTCTGGTGAGGGTGTTCAGCAGGCATTATTGAAAATGCTTGAAGGAACT
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aaccgtttctgcccttttctactgactttcacgccctcagttataattttct--ttgaatgcagcttcgcaactcaatactgacactcagtgtatggtt-cagGCTGAGAGTAAAAATATTAGTCGGGATGTATCTGGTGAAGGTGTTCAGCAGGCACTATTGAAGATGCTTGAAGGCACTMapped 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|16276814|gb|BI942058.1|BI942058EST: CTCAACAAGGAATAATTTACATTGATGAAGTTGACAAAATAACGAAGAAG TCCAAGAGCTTAAATATCAGTCGGGATGTTTCTGGTGAGGGTGTTCAGCAG
genomic: CTCAACAAGGAATAATTTACATTGATGAAGTTGACAAAATAACGAAGAAGgtttcttttc ... ataattacagTCCAAGAGCTTAAATATCAGTCGGGATGTTTCTGGTGAGGGTGTTCAGCAG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.agttaatactttcttgttgactatagattttaatgttgttgttatataattacagTCCAAGAGCTTAAATATCAGTCGGGATGTTTCTGGTGAGGGTGTTCAGCAGGCATTATTGAAAATGCTTGAAGGAACT
ttttaat putative branch site (score: 3)
tatagattttaatgtt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtttcttttctaatttaattggataagttaatactttcttgttgactatagattttaatgttgttgttatataattacagTCCAAGAGCTTAAATATCAGTCGGGATGTTTCTGGTGAGGGTGTTCAGCAGGCATTATTGAAAATGCTTGAAGGAACT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA