Sequence
atgc intronic sequence ATGC exonic sequence...tctcctattgtccgtttgtctacatttctgaagcttgttctccatttacaattacctttttgtttttttaattacttaaaattgctatcatctttcacagATTATTGCCATCAAGGATATCATACGACCCCCCAAAAAGGAGACCTTCAATGATGTGTACATTGTTTATGAATTGATGGACACTGATCTTCATCATATAA
Basic information
species | Glycine max |
transcript | GLYMA08G02060.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA08G02060.1 (Glycine max), 3'ss of exon 2
lower sequence: LOC_Os10g38950.1 (Oryza sativa), 3'ss of exon 2
tctcctattgtccgtttgtctacatttctgaagcttgttctccatttacaatt---acctttttgtttttttaattacttaaaattgctatcatctttcacagATTATTGCCATCAAGGATATCATACGACCCCCCAAAAAGGAGACCTTCAATGATGTGTACATTGTTTATGAATTGATGGACACTGATCTTCATCATATAA
|||| || | ||||| || ||| ||| | ||||| | | || ||| | | | | | | ||| | | ||||||||||||||||| ||||| || || || ||||| | || || | ||| |||||||| |||||||||| ||| |||||||| |||||||| ||||| || |
-ttccttttttt--tttgttgggcggtcaagagcgtgtgatacatttttgactcacacatttatatcatatagtctgatggtgattttaacactggatcacagATTATTGCCATAAAGGACATAATTCGCCCCCCAAGAAGAGACAACTTTAATGATGTTTACATTGTTTCTGAGTTGATGGATACTGATCTCCATCAGATCA
upper sequence: GLYMA08G02060.1 (Glycine max), 3'ss of exon 2
lower sequence: LOC_Os08g06060.1 (Oryza sativa), 3'ss of exon 2
-tctcctattgtccgtttgtctacatttctgaagcttgttctccatttacaattacctttttgtttttttaattacttaaaattgctatcatctttcacagATTATTGCCATCAAGGATATCATACGACCCCCCAAAAAGGAGACCTTCAATGATGTGTACATTGTTTATGAATTGATGGACACTGATCTTCATCATATAA
||| ||| | | ||| | || | || | | |||| | | ||| |||| | | || ||| | ||| |||||||| | || | || ||||| |||||||| || || | | ||||| |||||||||||| |||||||| ||||| | ||||||||||||||||| || |
gtcttttatc-ttggcaatactagggattgttagatgattagatagtaacaagaaacaattttttttgtgacttgtgacaaaatctagccatttttcacagGTCATCTCAATAAAGGACATCATACGGCCACCAAGGAGGGAGAACTTCAATGATGTCTACATTGTCTATGAGCTCATGGACACTGATCTTCACCACCTTC
upper sequence: GLYMA08G02060.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv02s0025g00270.t01 (Vitis vinifera), 3'ss of exon 2
tctcctattgtccgtttgtctacatttctgaagcttgttctccatttacaattacctttttgtttttttaattacttaaaattgctatca---tctttc------acagATTATTGCCATCAAGGATATCATACGACCCCCCAAAAAGGAGACCTTCAATGATGTGTACATTGTTTATGAATTGATGGACACTGATCTTCATCATATAA
| | | || | | | |||| | | | || ||| || |||| ||| || | | || | ||| | | |||||| |||| |||||||||||||||| || |||||||| || || ||||| || ||||||||||| |||||||||||||||||||||||||||||||||||||| || |
--------tttgccttgttatgtttgtctgggagtgtgtgtacagttatcatgacctattttttcgcctgaa-acatggaatcattgcccagttctttccttgccacagGTTATTGCCATCAAGGACATTATACGACCACCAAAGAAGGAAACTTTCAATGATGTCTACATTGTTTATGAATTGATGGACACTGATCTTCATCAGATCAMapped 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|213589538|gb|DB973209.1|DB973209EST: AGAGAACATTGAGAGAAATCAAGCTCCTTCGTCACATGGACCATGATAAT ATTATTGCCATCAAGG
genomic: AGAGAACATTGAGAGAAATCAAGCTCCTTCGTCACATGGACCATGATAATgtaagtgctc ... tctttcacagATTATTGCCATCAAGG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttacaattacctttttgtttttttaattacttaaaattgctatcatctttcacagATTATTGCCATCAAGGATATCATACGACCCCCCAAAAAGGAGACCTTCAATGATGTGTACATTGTTTATGAATTGATGGACACTGATCTTCATCATATAA
ttttaat putative branch site (score: 3)
tcatctttc putative PPT
tttttgtttttttaat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tctcctattgtccgtttgtctacatttctgaagcttgttctccatttacaattacctttttgtttttttaattacttaaaattgctatcatctttcacagATTATTGCCATCAAGGATATCATACGACCCCCCAAAAAGGAGACCTTCAATGATGTGTACATTGTTTATGAATTGATGGACACTGATCTTCATCATATAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA
- -cctattg
- - - - - - - - - -ctacatt
- - - - - - - - - - - - - -ctgaagc
- - - - - - - - - - - - - - - - - - -ttctcca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgctatc