Sequence
atgc intronic sequence ATGC exonic sequence...tgtttacttctgttaattttttaatgccttgtttattaatagttgtacaccaaatttgccatctgatttcatcactctttcttttcccattgtatggcagGAGCATTTGTTAATAGTATGTGAGCTACTTAAAGCAAACTTGTATGAGTTTCATAAATTTAATAGAGAATCAGGTGGTGAAGTGTACTTTACAATGCCAA
Basic information
species | Glycine max |
transcript | GLYMA08G06160.1 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA08G06160.1 (Glycine max), 3'ss of exon 5
lower sequence: LOC_Os03g51020.1 (Oryza sativa), 3'ss of exon 3
tgtttacttctgttaattttttaatgccttgtttattaatagt------tgtacaccaaattt--gccatctgatttcatcactctttcttttcccattgtatggcagGAGCATTTGTTAATAGTATGTGAGCTACTTAAAGCAAACTTGTATGAGTTTCATAAATTTAATAGAGAATCAGGTGGTGAAGTGTACTTTACAATGCCAA
||||| | | || | || | ||||| | | | | ||||||| | ||| || || || || | |||| | |||||| |||||| | ||||| |||||||| || || ||||| |||||||| ||||| || || || ||||||||||| || || || || || ||||||||||
------gttctgagactattcttcaagctgatgtattaggactgtctgatatctttcaaatttatgtcattacatcctataacaaatt--tgaagcatttgtttgcagGAACATTTGCTTATAGTCTGTGAGCTTCTGAAGGCAAATTTGTATGAATTTCAAAAGTTCAACAGAGAATCAGGAGGCGAGGTCTATTTCACAATGCCAA
upper sequence: GLYMA08G06160.1 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM2G181002_T01 (Zea mays), 3'ss of exon 3
-tgtttacttctgttaattttttaatgc-cttgtttattaatagttgtacaccaaatttgccatctgatttcatcactctttcttttcc-cattgtatggcagGAGCATTTGTTAATAGTATGTGAGCTACTTAAAGCAAACTTGTATGAGTTTCATAAATTTAATAGAGAATCAGGTGGTGAAGTGTACTTTACAATGCCAA
| ||| | | | | ||| || | | | | | || | ||| || | || || | ||| || |||| |||||| || |||||||||||| | ||||| ||||| || || || ||||| |||| |||||||| ||||| || ||||||||||| ||||| || ||||| ||||||||||
taaatgactcttctccaaaacaaattgctctcgagtcacagca-tcatataataaagtttgt-tgtgtttgctgtactacttattttaaacattgtttg-cagGAGCATTTGCTGATAGTCTGTGAACTTCTGAAGGCAAATCTGTACGAGTTTCAGAAATTCAACAGAGAATCAGGGGGTGAGGTTTACTTCACAATGCCAA
upper sequence: GLYMA08G06160.1 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM2G015073_T01 (Zea mays), 3'ss of exon 3
---tgtttacttctgttaattttttaatgccttgtttattaatagttgtacaccaaatttgccatctgatttcatcactctttcttttcccattgtatggcagGAGCATTTGTTAATAGTATGTGAGCTACTTAAAGCAAACTTGTATGAGTTTCATAAATTTAATAGAGAATCAGGTGGTGAAGTGTACTTTACAATGCCAA
|| | || || | | || | ||| || | | | ||| | | | | || | |||| || | | ||| || ||||| |||||| | ||||| ||||| || || || ||||| ||||||||||||| ||||| || ||||||||||| ||||| || ||||| ||||||||||
ggaatttcagagctcagggttgataattggttcttttccaaagcaatttgccttaaagtcacaacatttctttaccacttatt--tcaaatactgtttg-cagGAACATTTGCTGATAGTCTGTGAACTTCTGAAGGCAAATCTGTATGAGTTTCAGAAATTCAACAGAGAATCAGGGGGTGAGGTTTACTTCACAATGCCAA
upper sequence: GLYMA08G06160.1 (Glycine max), 3'ss of exon 5
lower sequence: AT1G73450.1 (Arabidopsis thaliana), 3'ss of exon 3
---------------------------------------------------------------------------------tgtttacttctgttaattttttaatgccttgtttattaatagttgtacaccaaatttgccatctgatttcatcactctttc---ttttcccattgta--tggcagGAGCATTTGTTAATAGTATGTGAGCTACTTAAAGCAAACTTGTATGAGTTTCATAAATTTAATAGAGAATCAGGTGGTGAAGTGTACTTTACAATGCCAA
|||| | | ||||||| || |||||| | | || | || | | || || | | | | || | | ||| | ||||||||| ||| |||| |||||||| || ||||| || || | || ||||| || |||||||| |||||||||||||||||||| || || || |||||||
gtaagtgattacatcccttttgcaaaatttggttttgctactgtatatcaaaagtgaccaattgtgtctttctcttcaacaattttagcacaagtgtgaaccatatgcctt-ttatttaatacctttgcaatat-ttctctttgtggattgtttggtgtaacggattccctgaatgttctttgcagGAGCACTTGCTAATTGTATGTGAACTTCTTAAGGCCAATCTATACGAGTTCCACAAATTTAACAGAGAATCAGGTGGTGAAGTTTATTTCACGATGCCAA
upper sequence: GLYMA08G06160.1 (Glycine max), 3'ss of exon 5
lower sequence: AT3G17750.1 (Arabidopsis thaliana), 3'ss of exon 4
-------------------------------------------------------------------tgtttacttctgttaattttttaatgccttgtttattaatagttgtacaccaaatttgccatctgatt--tcatcactctttcttttcccattgtatggcagGAGCATTTGTTAATAGTATGTGAGCTACTTAAAGCAAACTTGTATGAGTTTCATAAATTTAATAGAGAATCAGGTGGTGAAGTGTACTTTACAATGCCAA
|| | | | | |||| || || | | | | | || || | | || ||| | | | || || || || | ||||||||| |||||||||||||||| || || || ||||||||||||||||| || || |||||||| |||||||| || || || || || || |||||||
gtaagtagatagatgcagaattgtatctttttcttttcaacaccgggtggatattctgctgctttggtgctatgatgtatcaattgttcgattcagtaaagaacatgggacgtgagcctacatcatgatgccattgactgtgattaattggaatctca--gttttgcagGAGCACCTGTTAATAGTATGTGAACTTCTCAAGGCAAACTTGTATGAGTTCCAAAAGTTTAATAGGGAATCAGGGGGAGAGGTTTATTTCACTATGCCAA
upper sequence: GLYMA08G06160.1 (Glycine max), 3'ss of exon 5
lower sequence: AT1G73460.1 (Arabidopsis thaliana), 3'ss of exon 3
tgtttacttctgttaattttttaatgccttgttta--ttaatagttgtacaccaaatttgccatctgattt-catcactctttcttttcccattgtatggcagGAGCATTTGTTAATAGTATGTGAGCTACTTAAAGCAAACTTGTATGAGTTTCATAAATTTAATAGAGAATCAGGTGGTGAAGTGTACTTTACAATGCCAA
|| | | | | |||| | || || | | || | | |||| || || | || ||| | || | || |||||||| ||| |||| |||||||| || ||||| || || | || || || || |||||||| |||||||||||||||||||| || || || |||||||
-attgaaatataaaggggtcataataaactaagtaggtttgcattattatatctc-tttgtggattgtttggtgtaacggattccctgaatgttctttg-cagGAGCACTTGCTAATTGTATGTGAACTTCTTAAGGCCAATCTATACGAATTCCACAAATTTAACAGAGAATCAGGTGGTGAAGTTTATTTCACGATGCCAA
upper sequence: GLYMA08G06160.1 (Glycine max), 3'ss of exon 5
lower sequence: Vv01s0011g01590.t01 (Vitis vinifera), 3'ss of exon 9
-tgtttacttctgttaattttttaatgccttgtttattaatagttgtacaccaaatttgccatctgatttcatcactctttcttttcccattgtatggcagGAGCATTTGTTAATAGTATGTGAGCTACTTAAAGCAAACTTGTATGAGTTTCATAAATTTAATAGAGAATCAGGTGGTGAAGTGTACTTTACAATGCCAA
| ||| | | | ||| | || | | | | | | | | |||| || | || ||| || || || || | | |||||| ||||| ||||| ||||| || || || || |||||||||||||||||||||||||||||||||||||| || || || || ||||| ||||||||||
gtttttgccatcat-agtttatgcatttatggatgtctccaatatatgattttacagtgcctgctcaattagtcaggagtttactttcctttattttgcagGAACATTTATTAATTGTATGCGAACTTCTCAAGGCAAACTTGTATGAGTTTCATAAATTTAATAGAGAATCCGGAGGGGAGGTTTACTTCACAATGCCAA
upper sequence: GLYMA08G06160.1 (Glycine max), 3'ss of exon 5
lower sequence: PP1S47_312V6.1 (Physcomitrella patens), 3'ss of exon 4
-------------------tgtttacttctgttaattttttaatgccttgtt-tatta----atagttgtacaccaaatttgccatctgatttcatcactctttcttttcccattgt--atggcagGAGCATTTGTTAATAGTATGTGAGCTACTTAAAGCAAACTTGTATGAGTTTCATAAATTTAATAGAGAATCAGGTGGTGAAGTGTACTTTACAATGCCAA
|| | | || | | | | | ||| || | ||| ||| | ||| | || | | | | || | || || || |||||||||||||| ||||| |||||| ||||| ||| || ||||| ||||| || |||| || ||||||||||||||||| ||||||||||| |||||
gtaatcacagtggcttttgtgctacatgttgatgaatcatacgaactacgttatactgcagcatatgtgtgctttttctttctcctcgtactgactaaggctagatattggtggtggcgatttcagGAGCATTTGTTCATAGTTTGTGAGTTACTTCGAGCTAATTTGTACGAGTTCCACAAATACAACAGAGAATCAGGTGGTGAGGTGTACTTTACGATGCCCC
upper sequence: GLYMA08G06160.1 (Glycine max), 3'ss of exon 5
lower sequence: PP1S381_39V6.1 (Physcomitrella patens), 3'ss of exon 11
-------------------------------------------------------------------------------tgtttacttctgt-----taattttttaatgccttgtttattaatagttgtacaccaaatttgccatctgatttcatcact---ctttcttttcccattgt----atggcagGAGCATTTGTTAATAGTATGTGAGCTACTTAAAGCAAACTTGTATGAGTTTCATAAATTTAATAGAGAATCAGGTGGTGAAGTGTACTTTACAATGCCAA
|| || | ||| | ||| | | | | | | |||||||| |||||| | | || || | | | | | || || | ||||||| |||| || || |||||| ||||| ||| ||| | || ||||||||||||| || |||||||||||||| || ||||||||||| |||||
gtaattagggtggcctttttgttgcatgtctttgagccatgcggacttctctgtactgtagaaagtgaatgtacacctacgtatagctgtgtgcgtgcgagtttgtggaggcgcgcaagcgagtgtgtgtacacc---tttgcctttggtttatataggtaagcgctaaatattggtggtggtgattgtagGAGCACCTGTTCATCGTTTGTGAGTTACTTCGAGCTAACCTATACGAGTTTCATAAATACAACAGAGAATCAGGTGGCGAGGTGTACTTTACGATGCCCC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tacaccaaatttgccatctgatttcatcactctttcttttcccattgtatggcagGAGCATTTGTTAATAGTATGTGAGCTACTTAAAGCAAACTTGTATGAGTTTCATAAATTTAATAGAGAATCAGGTGGTGAAGTGTACTTTACAATGCCAA
atctgat putative branch site (score: 4)
tttcatcactctttct CT-rich tract
tttctttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tgtttacttctgttaattttttaatgccttgtttattaatagttgtacaccaaatttgccatctgatttcatcactctttcttttcccattgtatggcagGAGCATTTGTTAATAGTATGTGAGCTACTTAAAGCAAACTTGTATGAGTTTCATAAATTTAATAGAGAATCAGGTGGTGAAGTGTACTTTACAATGCCAA
- - -acttctg
- - - - - - - - - - - aatgcct
- - - - - - - - - - - - - - - - - - - - - - - -caccaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - tttgcca