Sequence
atgc intronic sequence ATGC exonic sequence...gtttacttctgttaatttttgaatggccttgtttatttatagttctacaccaaatttgtcatctaactttatcactctttcttttcccattgtatggcagGAACATTTGTTAATAGTATGTGAACTACTTAAAGCAAACTTGTATGAGTTTCATAAATTTAATAGAGAATCAGGTGGTGAAGTGTACTTTACAATGCCAA
Basic information
species | Glycine max |
transcript | GLYMA05G33560.1 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA05G33560.1 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os03g51020.1 (Oryza sativa), 3'ss of exon 3
gtttacttctgttaatttttgaatggccttgttt--atttatagttctacaccaaattt--gtcatctaactttatcactctttcttttcccattgtatggcagGAACATTTGTTAATAGTATGTGAACTACTTAAAGCAAACTTGTATGAGTTTCATAAATTTAATAGAGAATCAGGTGGTGAAGTGTACTTTACAATGCCAA
| || || | || | | | || | | | | | ||||||| ||||| | ||| || || | |||| | ||||||||||||| | ||||| ||||| || || || ||||| |||||||| ||||| || || || ||||||||||| || || || || || ||||||||||
--gttctgagactattcttcaagctgatgtattaggactgtctgatatctttcaaatttatgtcattacatcctataacaaatt--tgaagcatttgtttgcagGAACATTTGCTTATAGTCTGTGAGCTTCTGAAGGCAAATTTGTATGAATTTCAAAAGTTCAACAGAGAATCAGGAGGCGAGGTCTATTTCACAATGCCAA
upper sequence: GLYMA05G33560.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G015073_T01 (Zea mays), 3'ss of exon 3
----gtttacttctgttaatttttgaatggccttgtttatttatagttctacaccaaatttgtcatctaactttatcactctttcttttcccattgtatggcagGAACATTTGTTAATAGTATGTGAACTACTTAAAGCAAACTTGTATGAGTTTCATAAATTTAATAGAGAATCAGGTGGTGAAGTGTACTTTACAATGCCAA
|| | || || | | ||| | || | || | | ||| | | | ||||| |||| || | | ||| || |||||||||||| | ||||| |||||||| || || ||||| ||||||||||||| ||||| || ||||||||||| ||||| || ||||| ||||||||||
ggaatttcagagctcagggttgataattggttcttttccaaagcaatt-tgccttaaagtcacaacatttctttaccacttatt--tcaaatactgtttg-cagGAACATTTGCTGATAGTCTGTGAACTTCTGAAGGCAAATCTGTATGAGTTTCAGAAATTCAACAGAGAATCAGGGGGTGAGGTTTACTTCACAATGCCAA
upper sequence: GLYMA05G33560.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G181002_T01 (Zea mays), 3'ss of exon 3
--gtttacttctgttaatttttgaatggccttgtttatttatagttctacaccaaatttgtcat-ctaactttatcactctttcttttcccattgtatggcagGAACATTTGTTAATAGTATGTGAACTACTTAAAGCAAACTTGTATGAGTTTCATAAATTTAATAGAGAATCAGGTGGTGAAGTGTACTTTACAATGCCAA
| ||| | | | | || || | | | | || ||||| | | || || ||| || || |||||| || ||||| |||||| | ||||| |||||||| || || ||||| |||| |||||||| ||||| || ||||||||||| ||||| || ||||| ||||||||||
taaatgactcttctccaaaacaaattgctctcgagtcacagcatcatataataaagtttgttgtgtttgctgtactacttatt--ttaaacattgtttg-cagGAGCATTTGCTGATAGTCTGTGAACTTCTGAAGGCAAATCTGTACGAGTTTCAGAAATTCAACAGAGAATCAGGGGGTGAGGTTTACTTCACAATGCCAA
upper sequence: GLYMA05G33560.1 (Glycine max), 3'ss of exon 3
lower sequence: AT1G73450.1 (Arabidopsis thaliana), 3'ss of exon 3
-----------------------------------------------------------------------------gtttacttctgttaatttttgaatggccttgtttatttatagt-tctacaccaaatttgtcatc-taactttatcactctttc---ttttcccattgta--tggcagGAACATTTGTTAATAGTATGTGAACTACTTAAAGCAAACTTGTATGAGTTTCATAAATTTAATAGAGAATCAGGTGGTGAAGTGTACTTTACAATGCCAA
| || | | | |||| | || | | || | || | | |||| || | | || | | | | || | | ||| | |||||| || ||| |||| ||||||||||| ||||| || || | || ||||| || |||||||| |||||||||||||||||||| || || || |||||||
gtaagtgattacatcccttttgcaaaatttggttttgctactgtatatcaaaagtgaccaattgtgtctttctcttcaacaattttagcacaagtgtgaaccatatgccttttatttaatacctttgcaatatttctctttgtggattgtttggtgtaacggattccctgaatgttctttgcagGAGCACTTGCTAATTGTATGTGAACTTCTTAAGGCCAATCTATACGAGTTCCACAAATTTAACAGAGAATCAGGTGGTGAAGTTTATTTCACGATGCCAA
upper sequence: GLYMA05G33560.1 (Glycine max), 3'ss of exon 3
lower sequence: AT3G17750.1 (Arabidopsis thaliana), 3'ss of exon 4
-------------------------------------------------------------gtttacttctgttaatttttgaatggccttgtttatt------tatagttc-tacaccaaatttgtcatctaact--ttatcactctttcttttcccattgtatggcagGAACATTTGTTAATAGTATGTGAACTACTTAAAGCAAACTTGTATGAGTTTCATAAATTTAATAGAGAATCAGGTGGTGAAGTGTACTTTACAATGCCAA
||| | || | || | | ||| | || | | || | | | || | | | || | | | | | | || || || || | |||||| || ||||||||||||||||||| || || ||||||||||||||||| || || |||||||| |||||||| || || || || || || |||||||
gtaagtagatagatgcagaattgtatctttttcttttcaacaccgggtggatattctgctgctttggtgctat-gatgtatcaattgttcgattcagtaaagaacatgggacgtgagcctacatcatgatgccattgactgtgattaattggaatctca--gttttgcagGAGCACCTGTTAATAGTATGTGAACTTCTCAAGGCAAACTTGTATGAGTTCCAAAAGTTTAATAGGGAATCAGGGGGAGAGGTTTATTTCACTATGCCAA
upper sequence: GLYMA05G33560.1 (Glycine max), 3'ss of exon 3
lower sequence: AT1G73460.1 (Arabidopsis thaliana), 3'ss of exon 3
gtttacttctgttaatttttgaatggcctt-gtttatttatagttctacaccaaatttgtcatctaactt-tatcactctttcttttcccattgtatggcagGAACATTTGTTAATAGTATGTGAACTACTTAAAGCAAACTTGTATGAGTTTCATAAATTTAATAGAGAATCAGGTGGTGAAGTGTACTTTACAATGCCAA
|| | | | | ||| || || ||| | | || | | ||||| | | | | || ||| | || | || ||||| || ||| |||| ||||||||||| ||||| || || | || || || || |||||||| |||||||||||||||||||| || || || |||||||
attgaaatataaaggggtcataataaactaagtaggtttgcattattatatctc-tttgtggattgtttggtgtaacggattccctgaatgttctttg-cagGAGCACTTGCTAATTGTATGTGAACTTCTTAAGGCCAATCTATACGAATTCCACAAATTTAACAGAGAATCAGGTGGTGAAGTTTATTTCACGATGCCAA
upper sequence: GLYMA05G33560.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv01s0011g01590.t01 (Vitis vinifera), 3'ss of exon 9
gtttacttctgttaatttttgaatggccttgtttatttatagt-tctacaccaaatttgtcatctaactttatcactctttcttttcccattgtatggcagGAACATTTGTTAATAGTATGTGAACTACTTAAAGCAAACTTGTATGAGTTTCATAAATTTAATAGAGAATCAGGTGGTGAAGTGTACTTTACAATGCCAA
|||| | | | | ||| || | | | | | | | | || | || | || ||| || || || || | | |||||||||||| ||||| ||||| ||||| || || |||||||||||||||||||||||||||||||||||||| || || || || ||||| ||||||||||
gttt-ttgccatcatagtttatgcatttatggatgtctccaatatatgattttacagtgcctgctcaattagtcaggagtttactttcctttattttgcagGAACATTTATTAATTGTATGCGAACTTCTCAAGGCAAACTTGTATGAGTTTCATAAATTTAATAGAGAATCCGGAGGGGAGGTTTACTTCACAATGCCAA
upper sequence: GLYMA05G33560.1 (Glycine max), 3'ss of exon 3
lower sequence: PP1S47_312V6.1 (Physcomitrella patens), 3'ss of exon 4
--------gtttacttctgt--taatttttgaatggccttgtttatt-tatagttctacaccaaatttgtcatctaactttatcactctttct--------tttcccattgt--------atggcagGAACATTTGTTAATAGTATGTGAACTACTTAAAGCAAACTTGTATGAGTTTCATAAATTTAATAGAGAATCAGGTGGTGAAGTGTACTTTACAATGCCAA
| ||| ||| || | |||| | | | | | | || || || || ||| | | |||| || ||| | || | |||| || ||||| |||||||| ||||| ||||| ||||| ||| || ||||| ||||| || |||| || ||||||||||||||||| ||||||||||| |||||
gtaatcacagtggcttttgtgctacatgttgatgaatcatacgaactacgttatactgcagcatatgtgtgctttttctttctc-ctcgtactgactaaggctagatattggtggtggcgatttcagGAGCATTTGTTCATAGTTTGTGAGTTACTTCGAGCTAATTTGTACGAGTTCCACAAATACAACAGAGAATCAGGTGGTGAGGTGTACTTTACGATGCCCC
upper sequence: GLYMA05G33560.1 (Glycine max), 3'ss of exon 3
lower sequence: PP1S381_39V6.1 (Physcomitrella patens), 3'ss of exon 11
--------------------------------------------------------------------------------------gtttacttctgttaatttttgaatggccttgtttatttata-gttctacaccaaatttgtcatcta-actttatcactctttcttttcccattgtatggcagGAACATTTGTTAATAGTATGTGAACTACTTAAAGCAAACTTGTATGAGTTTCATAAATTTAATAGAGAATCAGGTGGTGAAGTGTACTTTACAATGCCAA
| | || | ||| || | | | | | || | | |||| | || | | | | || | || || | |||| || |||| || || ||||| ||||| ||| ||| | || ||||||||||||| || |||||||||||||| || ||||||||||| |||||
gtaattagggtggcctttttgttgcatgtctttgagccatgcggacttctctgtactgtagaaagtgaatgtacacctacgtatagctgtgtgcgtgcgagtttgtggaggcgcgcaagcgagtgtgtgtacacctttgcctttggtttatataggtaagcgctaaatattggtggtggtgattgtagGAGCACCTGTTCATCGTTTGTGAGTTACTTCGAGCTAACCTATACGAGTTTCATAAATACAACAGAGAATCAGGTGGCGAGGTGTACTTTACGATGCCCCMapped 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|192295803|gb|FG992614.1|FG992614EST: CTGCAGACAAGTATCACATTCTTCGATTATATGATTATTTCTATTATCGA GAACATTTGTTAATAGTATGTGAACTACTTAAAGCAAACTTGTATGAGTTT
genomic: CTGCAGACAAGTATCACATTCTTCGATTATATGATTATTTCTATTATCGAgtaagtggat ... tgtatggcagGAACATTTGTTAATAGTATGTGAACTACTTAAAGCAAACTTGTATGAGTTT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tacaccaaatttgtcatctaactttatcactctttcttttcccattgtatggcagGAACATTTGTTAATAGTATGTGAACTACTTAAAGCAAACTTGTATGAGTTTCATAAATTTAATAGAGAATCAGGTGGTGAAGTGTACTTTACAATGCCAA
atctaac putative branch site (score: 2)
ctttatcactctttct CT-rich tract
taactttat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtttacttctgttaatttttgaatggccttgtttatttatagttctacaccaaatttgtcatctaactttatcactctttcttttcccattgtatggcagGAACATTTGTTAATAGTATGTGAACTACTTAAAGCAAACTTGTATGAGTTTCATAAATTTAATAGAGAATCAGGTGGTGAAGTGTACTTTACAATGCCAA
- - acttctg
- - - - - - - - - - - - ggccttg
- - - - - - - - - - - - - - - - - - - - - - ctacacc