Sequence
atgc intronic sequence ATGC exonic sequence...ccagataagagcccgtctgtggaaagttatggttttatacaagttactccaatctctggatgtaaattctcataagcatgttaatccttttctttttcagATCCCAATAGAATGTTTTGAGGAACCATGGGTCATTTTTCGAGGGAAAGATGGGAAGCCTGGATGTGTTCAAAATACCTGCGCACACAGAGCATGCCCTC
Basic information
species | Glycine max |
transcript | GLYMA06G11920.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA06G11920.1 (Glycine max), 3'ss of exon 4
lower sequence: LOC_Os10g41760.1 (Oryza sativa), 3'ss of exon 4
ccagataagagcccgtctgtggaaagttatggttttatacaagttactccaatctctggatgtaaattctcataa-gcatgttaat----ccttttctttttcagATCCCAATAGAATGTTTTGAGGAACCATGGGTCATTTTTCGAGGGAAAGATGGGAAGCCTGGATGTGTTCAAAATACCTGCGCACACAGAGCATGCCCTC
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--------------------gtaacgcaatgaatg-attcaggcatttacaatgtccgga-gtaccagttaatgatatgttttgatgtggtctgtgtgttctcagGTACCAATAGATTGTTTTGAGGAGCAGTGGGTAATTTTCCGAGGAAAGGATGGGAGACCTGGATGTGTTCAGAACACATGTGCTCACAGAGCCTGCCCTC
upper sequence: GLYMA06G11920.1 (Glycine max), 3'ss of exon 4
lower sequence: LOC_Os10g41780.1 (Oryza sativa), 3'ss of exon 4
ccagataagagcccgtctgtggaaagttatggttttatacaagttactccaatctctggatgtaaattctcataagcatgttaatcctttt---ctttttcagATCCCAATAGAATGTTTTGAGGAACCATGGGTCATTTTTCGAGGGAAAGATGGGAAGCCTGGATGTGTTCAAAATACCTGCGCACACAGAGCATGCCCTC
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----gtaaaaaca-acgtgcg---attcaggcatttttttacgaggtcagagttagcagttgcagaaacttatgtttatttgatgtggtttgcgcattctcagGTGCCAATAGATTGTTTTGAGGAGCAGTGGGTAATTTTCCGAGGAAAGGATGGGAGACCTGGATGTGTTATGAACACATGTGCTCACAGAGCTTGCCCTC
upper sequence: GLYMA06G11920.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv18s0001g02700.t01 (Vitis vinifera), 3'ss of exon 3
--------------------------------------------------------------------------------------ccagataagagcccgtctgtggaaagttatggttttatacaagttactccaatctctggatgtaaattctcataagcatgttaatccttttctttttcagATCCCAATAGAATGTTTTGAGGAACCATGGGTCATTTTTCGAGGGAAAGATGGGAAGCCTGGATGTGTTCAAAATACCTGCGCACACAGAGCATGCCCTC
|| | || | | | | |||| | || || ||||| || | | | || ||| | || | | |||||| |||||||| ||||| || || ||||||||||| ||||| | ||||| ||| |||||||||| ||||||||||| | || |||||||| || |||||||||||||
gtaagccagttttccaaacatctaaggctcatatttagtgattaaatacagattttccacattgtggctactcaacaatgtcttaagtagcaataagagaggaggcaaacatttatagcttatctggccttgtgataatctgtgagttt---tccttgtaacagttttcacctttttctgtttcagATTCCAATTGATTGCTTTGAGGAACCGTGGGTTGTCTTTCGTGGGCAAGATGGGAAACCTGGATGTGTCCGTAACACCTGCGCCCATAGAGCATGCCCTC
upper sequence: GLYMA06G11920.1 (Glycine max), 3'ss of exon 4
lower sequence: PP1S290_42V6.1 (Physcomitrella patens), 3'ss of exon 3
-------------------------ccagataagagcccgt-ctgtggaaagttat--ggttttatacaagttactcca-------atctctggatgtaaattctcataa--gcatgttaatcctttt-----ctttttcagATCCCAATAGAATGTTTTGAGGAACCATGGGTCATTTTTCGAGGGAAAGATGGGAAGCCTGGATGTGTTCAAAATACCTGCGCACACAGAGCATGCCCTC
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gtgaagaccactcgtgactttttgtccagtattgtacatgcgttgtgaatctttgtctggtctttcaacagcctggccatgaacttatttgtcgctttaccctggcttaacgaaaggttgatcctgtaatgagctgtatcagGTGCCGTTTAATAGCTTTGAAGAAGCATGGGTTATTTTTCGAGGGAAAGATGGCCGTCCAGGATGCGTGCGAGATTCTTGCGCACACAGGGCATGTCCACMapped 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|51345324|gb|CO986057.1|CO986057EST: ATTTCTGGTACCCTGTAGCTTTCTCTACTGACTTGAAGGATGATACAATG ATCCCAATAGAATGTTTTGAGGAACCATGGGTCATTTTTCGAGGGAAAGAT
genomic: ATTTCTGGTACCCTGTAGCTTTCTCTACTGACTTGAAGGATGATACAATGgtaagtcaat ... tctttttcagATCCCAATAGAATGTTTTGAGGAACCATGGGTCATTTTTCGAGGGAAAGAT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.actccaatctctggatgtaaattctcataagcatgttaatccttttctttttcagATCCCAATAGAATGTTTTGAGGAACCATGGGTCATTTTTCGAGGGAAAGATGGGAAGCCTGGATGTGTTCAAAATACCTGCGCACACAGAGCATGCCCTC
tgttaat putative branch site (score: 3)
ttaatccttttctttt CT-rich tract
ttttcttttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ccagataagagcccgtctgtggaaagttatggttttatacaagttactccaatctctggatgtaaattctcataagcatgttaatccttttctttttcagATCCCAATAGAATGTTTTGAGGAACCATGGGTCATTTTTCGAGGGAAAGATGGGAAGCCTGGATGTGTTCAAAATACCTGCGCACACAGAGCATGCCCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCA
- - - - - - - -tctgtgg
- - - - - - - - - - - - - - - - - - - - - - - - - - -ctctgga
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gcatgtt