Sequence
atgc intronic sequence ATGC exonic sequence...ttctctatcttctgccctttctgtctttttttttatgttttagccacatgctacatagcttaatgttttatgaatgagcatttactttgttgctctgcagGTTGCTTGCGTTATGACAATTTGGAGTCAACTTCAACCTGAATATGCAGCAAATATGTGGAATGAAGCCTTGAACAAACGACTTGGAACTAAA
Basic information
species | Glycine max |
transcript | GLYMA14G02820.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA14G02820.1 (Glycine max), 3'ss of exon 4
lower sequence: LOC_Os01g58114.2 (Oryza sativa), 3'ss of exon 4
ttctctatcttctgccctttctgtctttttttttatgttttagccacatgctacatagcttaatgttttatgaatgagcatttactttgttgctctgcagGTTGCTTGCGTTATGACAATTTGGAGTCAACTTCAACCTGAATATGCAGCAAATATGTGGAATGAAGCCTTGAACAAACGACTTGGAACTAAA
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aattttaataccagatatagcaaggattgcttgcaaggttgagctatgcatttgagatttatttgctgattgtagtaacaaaatcttacgattggcctagGTTGCCTCTGTGATGACTATGTGGAACAAACTTCAACCAGAGTATGCTGCCAACATGTGGAAAGAAGCCCTTAACAAACGGCTTGGAACTAAG
upper sequence: GLYMA14G02820.1 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G139374_T02 (Zea mays), 3'ss of exon 4
-ttctctatcttc-tgccctttctgtctttttttttatgttttagccacatgctacatagcttaat-gttttatgaatgagcatttactttgttgctctgcagGTTGCTTGCGTTATGACAATTTGGAGTCAACTTCAACCTGAATATGCAGCAAATATGTGGAATGAAGCCTTGAACAAACGACTTGGAACTAAA
| ||||| | || | | ||| | || || || | | || | ||| | | ||| | | ||| || | | || || |||||||||| |||||||| | ||||| | |||||||| || ||||| || ||||||||||| |||||| | |||||||| |||||||||||
ggtttctattccagtttttcttttaacagtttaggtttgattctgcattgt-ttgaatggtttattagctttgttactgaa-atctttatgaatg-tccacagGTTGCTTCTGTTATGACTGTATGGAGCAAGCTTCAACCAGAGTATGCTGCTAATATGTGGAAAGAAGCCCTTAACAAACGGCTTGGAACTAAG
upper sequence: GLYMA14G02820.1 (Glycine max), 3'ss of exon 4
lower sequence: PP1S191_130V6.3 (Physcomitrella patens), 3'ss of exon 5
----------------------ttctctatcttctgccctttctgtctttttttt---tatgtttt-agccacatgctacatag-----cttaatgttttatgaatg---agcatttactttgttgctctg-cagGTTGCTTGCGTTATGACAATTTGGAGTCAACTTCAACCTGAATATGCAGCAAATATGTGGAATGAAGCCTTGAACAAACGACTTGGAACTAAA
||| || | |||| || |||| | | || || || | || | | || | ||| | | | | | || || ||||| || | | || ||||| |||| || | |||||||| | ||| |||||||||||||||||||| ||||| ||||| || || || |
gtaatttttttacattattgacagtagtattttaaatttgtcaggtctccacttgagatatgacatgaaccgtggactcaatggtcgtcctgtacatcttgtatatgctaaatactaagctggtgttggtgacagGTGGCATCTGCGATAACAATGTGGACTCGGTTACAACCTGATTTTGCTGCAAATATGTGGAATGAAGCTTTGAATAAACGCCTGGGTACAGAGMapped 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|120493627|gb|EH221794.1|EH221794EST: TTTAAATGGAAACTATCCACCCCCCTTGGATGCTAATGTG GTTGCTTGCGTTATGACAATTTGGAGTCAACTTCAACCTGAATATGCAGCA
genomic: TTTAAATGGAAACTATCCACCCCCCTTGGATGCTAATGTGgtattaattt ... tgctctgcagGTTGCTTGCGTTATGACAATTTGGAGTCAACTTCAACCTGAATATGCAGCA
EST:
gi|37996930|gb|CF808519.1|CF808519EST: GGATAGACACTTTAAATGGAAACTATCCACCCCCCTTGGATGCTAATGTG GTTGCTTGCGTTATGACAATTTGGAGTCAACTTCAACCTGAATATGCAGCA
genomic: GGATAGACACTTTAAATGGAAACTATCCACCCCCCTTGGATGCTAATGTGgtattaattt ... tgctctgcagGTTGCTTGCGTTATGACAATTTGGAGTCAACTTCAACCTGAATATGCAGCA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.acatgctacatagcttaatgttttatgaatgagcatttactttgttgctctgcagGTTGCTTGCGTTATGACAATTTGGAGTCAACTTCAACCTGAATATGCAGCAAATATGTGGAATGAAGCCTTGAACAAACGACTTGGAACTAAA
gcttaat putative branch site (score: 4)
ctttgtt putative PPT
ttaatgttttatgaat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ttctctatcttctgccctttctgtctttttttttatgttttagccacatgctacatagcttaatgttttatgaatgagcatttactttgttgctctgcagGTTGCTTGCGTTATGACAATTTGGAGTCAACTTCAACCTGAATATGCAGCAAATATGTGGAATGAAGCCTTGAACAAACGACTTGGAACTAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC
- - - -tcttctg
- - - - - - - ccctttc
- - - - - - - - - - - - - - - - - - - - - - -acatgct
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gaatgag