Sequence
atgc intronic sequence ATGC exonic sequence...tattgaatttttttaccttcaattggtttttgcattttgcttgatgatgtcaacaaatgggtttcacatgcaactaatggagcttttttcccctcggcagACTCAAGGACGTGAATCAATTGCTGCTAAACTTGTTGCGAACCTTATTACAAAAGCTGGGGCAGACCGTGTTCTCGCTTGTGACCTTCATTCAGGGCAGT
Basic information
species | Glycine max |
transcript | GLYMA05G06110.1 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA05G06110.1 (Glycine max), 3'ss of exon 3
lower sequence: AT2G35390.3 (Arabidopsis thaliana), 3'ss of exon 2
------------tattgaatttttttaccttcaattggtttttgcattttgcttgatgatgtcaacaaatgg--gtttcacatgcaactaatggagcttttttcccctcggcagACTCAAGGACGTGAATCAATTGCTGCTAAACTTGTTGCGAACCTTATTACAAAAGCTGGGGCAGACCGTGTTCTCGCTTGTGACCTTCATTCAGGGCAGT
| | ||| ||| |||| || | | |||| ||||| | | | | | ||| | | || | ||| | |||| | || | ||||| ||||| |||||||| |||||||| ||| | ||||| || ||||| || ||||||| ||||| || ||||| |||||||| ||||||||||| ||||
gtaaagtctctttgtgtggtttagctactttcacatgatatggagggtttg-ttgataac-ttagctattggtaatcttttctggataaaattgtatgttttgctgcttg-cagACACAAGGGCGTGAATCCATTGCTGCCAAATTGGTTGCAAATCTTATCACTGAAGCTGGTGCAGATCGAGTTCTTGCTTGTGATCTTCATTCAGGACAGT
upper sequence: GLYMA05G06110.1 (Glycine max), 3'ss of exon 3
lower sequence: AT1G32380.1 (Arabidopsis thaliana), 3'ss of exon 3
tattgaatttttttaccttcaattggtt-tttgcattttgcttgatgatgtcaacaa-atgggtttcacatgcaactaatggagcttttttcccctcggcagACTCAAGGACGTGAATCAATTGCTGCTAAACTTGTTGCGAACCTTATTACAAAAGCTGGGGCAGACCGTGTTCTCGCTTGTGACCTTCATTCAGGGCAGT
| |||| ||| | || | ||| | ||| ||| | | || || ||| | || || | ||||| ||||| |||||||| |||||||| ||| | || || |||||||| ||| |||| || ||||| | ||||| |||||||| ||||||||||| || |
---------------------gtaggttctttttgtcttcttcaatggtagatacagtatgtcaagtaatttcatctgatgtatctattgatgtttt--cagACACAAGGGCGTGAATCTATTGCTGCCAAATTGGTAGCAAACCTTATAACAGAAGCCGGTGCAGATAGGGTTCTGGCTTGTGATCTTCATTCAGGACAAT
upper sequence: GLYMA05G06110.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv02s0012g00530.t01 (Vitis vinifera), 3'ss of exon 3
tattgaatttttttaccttcaattggtttttgcattttgcttgatgatgtcaacaaatgggtttcacat-gcaactaatggagcttttttcccctcggcagACTCAAGGACGTGAATCAATTGCTGCTAAACTTGTTGCGAACCTTATTACAAAAGCTGGGGCAGACCGTGTTCTCGCTTGTGACCTTCATTCAGGGCAGT
| ||| | | || || | ||||| |||| | || | | | || || || | | || | || ||| ||||||||||| |||||||| ||||| |||||||||||||| || |||| || ||||| || || ||||||||||| |||||||| |||||||| |||||||
-actgagaaatgatgggttgaacaatctacgtcatttctaaattggatgctagaaatttacatgtaaattacatcttcttcatctgtatttttctcttcagACTCAAGGGCGTGAATCCATTGCAGCTAAACTTGTTGCAAATGTTATCACCAAAGCAGGTGCGGACCGTGTTCTTGCTTGTGATCTTCATTCTGGGCAGT
upper sequence: GLYMA05G06110.1 (Glycine max), 3'ss of exon 3
lower sequence: EFJ14005 (Selaginella moellendorffii), 3'ss of exon 2
tattgaatttttttaccttcaattggtttttgcattttgcttgatgatgtcaacaaatgggtttcacatgcaactaatggagcttttttcccctcggcagACTCAAGGACGTGAATCAATTGCTGCTAAACTTGTTGCGAACCTTATTACAAAAGCTGGGGCAGACCGTGTTCTCGCTTGTGACCTTCATTCAGGGCAGT
| | | |||| || | | || | | || | || |||||| ||||||||||||||||||| ||||| || || |||||||| || ||| | ||| |||| || || |||||||||| || || ||| | || || ||||||
-------------------------------gtagtcactgtgat----ccagctttttctttcaatctacacgtcgtgtgatgtttttc--------agACTCAAGGACGTGAATCGATTGCAGCAAAGCTTGTTGCAAATCTTTTGACAGAAGCCGGTGCGAACCGTGTTCTTGCATGCGACTTACACTCGGGGCAGGMapped 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|7925715|gb|AW831741.1|AW831741EST: ATATCACTGCTGTGATTCCCTACTTTGGATATGCCAGAGCTGATAGAAAG ACTCAAGGACGTGAATCAATTGCTGCTAAACTTGTTGCGAACCTTATTACA
genomic: ATATCACTGCTGTGATTCCCTACTTTGGATATGCCAGAGCTGATAGAAAGgcaagtattt ... ccctcggcagACTCAAGGACGTGAATCAATTGCTGCTAAACTTGTTGCGAACCTTATTACA
EST:
gi|58018515|gb|CX705257.1|CX705257EST: ATATCACTGCTGTGATTCCCTACTTTGGATATGCCAGAGCTGATAGAAAG ACTCAAGGACGTGAATCAATTGCTGCT-AACTTGTTTGCGAACCTTATTAC
genomic: ATATCACTGCTGTGATTCCCTACTTTGGATATGCCAGAGCTGATAGAAAGgcaagtattt ... ccctcggcagACTCAAGGACGTGAATCAATTGCTGCTAAACTTG-TTGCGAACCTTATTAC
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gatgtcaacaaatgggtttcacatgcaactaatggagcttttttcccctcggcagACTCAAGGACGTGAATCAATTGCTGCTAAACTTGTTGCGAACCTTATTACAAAAGCTGGGGCAGACCGTGTTCTCGCTTGTGACCTTCATTCAGGGCAGT
aactaat putative branch site (score: 2)
cttttttcccctcggc putative PPT
tttttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tattgaatttttttaccttcaattggtttttgcattttgcttgatgatgtcaacaaatgggtttcacatgcaactaatggagcttttttcccctcggcagACTCAAGGACGTGAATCAATTGCTGCTAAACTTGTTGCGAACCTTATTACAAAAGCTGGGGCAGACCGTGTTCTCGCTTGTGACCTTCATTCAGGGCAGT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - accttca
- - - - - - - - - - - - - - - tgcattt
- - - - - - - - - - - - - - - - - - -tgcttga
- - - - - - - - - - - - - - - - - - - - - - tgatgtc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -acatgca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ctaatgg