Sequence
atgc intronic sequence ATGC exonic sequence...atttttgtatgtagtggagctagttttcaagccttgacaattacttgtttgaaactttgtagtttagtgagtgctaacacattgattgtaaaatatgtagGTAACCAGCCATGAGACCAGTTTGGTGGCTCGATGTCGTAGAGTATATGCCCATGCTCATGATTATCATATTAATTCTATTTCAAATAACAG
Basic information
species | Glycine max |
transcript | GLYMA07G01440.1 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA07G01440.1 (Glycine max), 3'ss of exon 5
lower sequence: LOC_Os02g13110.2 (Oryza sativa), 3'ss of exon 5
--------------------------------------------------------------------------------------------atttttgtatgtag---tggagctagttttcaagccttgacaattacttgtttgaaactttgtagtttagtgagtgctaacacattgattgtaaaatatgtagGTAACCAGCCATGAGACCAGTTTGGTGGCTCGATGTCGTAGAGTATATGCCCATGCTCATGATTATCATATTAATTCTATTTCAAATAACAG
|||| | ||| | | || ||| ||| | | | | || | || | | || ||||| | | | || | |||| |||| || |||| || | | || | |||| || | |||||| | |||||||||||||| ||||||||||| ||||||||||| ||
gttgtacttaacccactttattcattatctcatctgtaatcgtgttgttctgtacagcaccaaatctggtgttcacatgtaaaataagtctccttttggcatgaatacttatagatagattttcttctt--atggcaaactgcacatatgattacaatata-tgagtatttattt-tcatttactatgtatgcagGTCACTGGCCAAGATTTGAACCTTGTACCAAGATGCCGGCGTGTATATTCACATGCTCATGATTACCATATTAATTCCATTTCAAATAATAG
upper sequence: GLYMA07G01440.1 (Glycine max), 3'ss of exon 5
lower sequence: LOC_Os06g36770.2 (Oryza sativa), 3'ss of exon 5
--------------------------------------------atttttgtatgtagtggagctagt-tttcaagcc--ttgacaattacttgtttgaaactttgtagtttagtg-agtgctaac-acattgattgtaaaatatgtagGTAACCAGCCATGAGACCAGTTTGGTGGCTCGATGTCGTAGAGTATATGCCCATGCTCATGATTATCATATTAATTCTATTTCAAATAACAG
|| ||| | | | |||| || ||| | || ||||| | | | | | ||| | | || |||| || | ||| |||| | || || || | | || ||| ||||||| | |||||||| |||||||||||||| |||||||| ||||| |||| || ||
gtagttgtacttaacctctatatatcttaatcaacagaagatgacttgatgtcttgatcagctctagcacatctagctggcatatgataacttgcacggcaacctatgatcaagtccaaaattgactgcatttcttat----catgcagGTTGCAAGTCAAGATGTGAACCTTGTTGCTAGATGTCGACGTGTATATGCACATGCTCATGATTACCATATTAACTCTATATCAACCAATAG
upper sequence: GLYMA07G01440.1 (Glycine max), 3'ss of exon 5
lower sequence: LOC_Os06g36770.1 (Oryza sativa), 3'ss of exon 5
-----------------------------------------atttttgtatgtagtggagctagt-tttcaagcc--ttgacaattacttgtttgaaactttgtagtttagtg-agtgctaac-acattgattgtaaaatatgtagGTAACCAGCCATGAGACCAGTTTGGTGGCTCGATGTCGTAGAGTATATGCCCATGCTCATGATTATCATATTAATTCTATTTCAAATAACAG
|| ||| | | | |||| || ||| | || ||||| | | | | | ||| | | || |||| || | ||| |||| | || || || | | || ||| ||||||| | |||||||| |||||||||||||| |||||||| ||||| |||| || ||
gttgtacttaacctctatatatcttaatcaacagaagatgacttgatgtcttgatcagctctagcacatctagctggcatatgataacttgcacggcaacctatgatcaagtccaaaattgactgcatttcttat----catgcagGTTGCAAGTCAAGATGTGAACCTTGTTGCTAGATGTCGACGTGTATATGCACATGCTCATGATTACCATATTAACTCTATATCAACCAATAG
upper sequence: GLYMA07G01440.1 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM2G069631_T02 (Zea mays), 3'ss of exon 5
-------------------------------------------------------------atttttgtatgtagtggagctagttttcaagccttgacaa--------ttacttgtttgaaactttgtagttta-gtgagtgctaacaca--------ttgattgtaaaatatgtagGTAACCAGCCATGAGACCAGTTTGGTGGCTCGATGTCGTAGAGTATATGCCCATGCTCATGATTATCATATTAATTCTATTTCAAATAACAG
|| | | | || ||||| ||||| | | | | | | | ||| | | | |||| ||| | | || | |||| |||| || |||| || | | || || || | | | |||||||||||||| ||||| || ||||||||||| ||||||||||| ||
gtagtacttaaacccacttcatctatcatctctaggttgtacaacatgaggaattagcattgcttgcatgtacaacacagtagtttttccccttgtgacagagaactagacattcttctaacagactatagataatatcagtgataattctgaatactttcctttactatttatgcagGTTACAGGCCAAGAATTTACTCATGTTGCGAGAAGCAGACGTGTATATGCCCATGCCCATGACTACCATATTAATTCCATTTCAAATAATAG
upper sequence: GLYMA07G01440.1 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM2G142334_T01 (Zea mays), 3'ss of exon 5
---------------------------------------------------------------------------------atttttgtatgtagtggagctagttt--tcaagccttgacaattact---tgtttga--aactttgtagtttagtgagtgcta-acacattgattgtaaaatat--gtagGTAACCAGCCATGAGACCAGTTTGGTGGCTCGATGTCGTAGAGTATATGCCCATGCTCATGATTATCATATTAATTCTATTTCAAATAACAG
|||| || | | | | ||| || | | | || || | | | | |||||| | || | || || || | | | |||| | | |||| || | ||| || || || | | || | || || ||||||||||| ||||| ||||| |||||||| ||||| || |||||||||||
gctgtacttaactcagtttcatttattcacctggcaaaaagcatattctaattatttagaaccattatgccattacctggaatttatgcagcgggaaaatgcattttagtcgattcatcgtccttcctgtctatgtaaccaactttttttttcacaatttgttacactgacccagtctaaactgtaaacagGTTACAACCCAAGAAACAAGCCTTGCTGCGAGTTGCCGAAGAGTATATGCTCATGCACATGACTATCATATAAATTCAATATCAAATAACAG
upper sequence: GLYMA07G01440.1 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM2G142334_T02 (Zea mays), 3'ss of exon 5
------------------------------------------------------------------------------------atttttgtatgtagtggagctagttt--tcaagccttgacaattact---tgtttga--aactttgtagtttagtgagtgcta-acacattgattgtaaa--atatgtagGTAACCAGCCATGAGACCAGTTTGGTGGCTCGATGTCGTAGAGTATATGCCCATGCTCATGATTATCATATTAATTCTATTTCAAATAACAG
|||| || | | | | ||| || | | | || || | | | | |||||| | || | || || || | | | |||| || |||| || | ||| || || || | | || | || || ||||||||||| ||||| ||||| |||||||| ||||| || |||||||||||
gtagctgtacttaactcagtttcatttattcacctggcaaaaagcatattctaattatttagaaccattatgccattacctggaatttatgcagcgggaaaatgcattttagtcgattcatcgtccttcctgtctatgtaaccaactttttttttcacaatttgttacactgacccagtctaaactgtaaacagGTTACAACCCAAGAAACAAGCCTTGCTGCGAGTTGCCGAAGAGTATATGCTCATGCACATGACTATCATATAAATTCAATATCAAATAACAG
upper sequence: GLYMA07G01440.1 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM2G165418_T02 (Zea mays), 3'ss of exon 6
-----------------atttttgtatgtagtggagctagttttcaagccttgaca---attacttgt--ttgaaactttgtagtttagtgagtgct------aacacattgattgt---aaaatatgtagGTAACCAGCCATGAGACCAGTTTGGTGGCTCGATGTCGTAGAGTATATGCCCATGCTCATGATTATCATATTAATTCTATTTCAAATAACAG
| || | ||| || | ||| || | | || || |||| | ||||| | || | | | | ||| |||| | | | ||||| |||| ||||| | || | | || ||| ||||||| | |||| ||| |||||||| ||||| ||||| ||||||||||||||||| ||
gtaagctatactcgacaacttatatat-tattaactttagcatttgaaattgtacttgtataacttttaagtgaaattatgcaaaactgcagctatttagtccaactcatttctctttcgaccatatgcagGTTACCAGTCTAGAAGCAAACCCTGTTGCTAGATGTCGACGTGTATTTGCTCATGCTCACGATTACCATATAAATTCTATTTCAAATAATAG
upper sequence: GLYMA07G01440.1 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM2G164185_T01 (Zea mays), 3'ss of exon 5
-----------------------------------------------------------------------atttttgtatgtagtggagctag--------tttt---caagccttgacaattacttgtttgaa-----actttgtagtttagtgagtgctaacac--attgattgtaaaatat--gtagGTAACCAGCCATGAGACCAGTTTGGTGGCTCGATGTCGTAGAGTATATGCCCATGCTCATGATTATCATATTAATTCTATTTCAAATAACAG
||| || || | ||| |||| |||| | || | ||| | ||| | | ||| | ||| | | | ||| | | | | |||| | | |||| || ||||| || || ||| | | | | || || ||||||||||| ||||| ||||| || ||||| ||||| || |||||||||||
gttgtacttaactcagtttcatttatgcaccttgcaaaaccatattgtagttatttagaactattgagctgattcctggatattgtgtagctgaaaattgtattttagttgattctaaaatatttcctgtctatgtaaccattttttcttttcacaatttgttacattgactcagtataaactgtaaacagGTTACAAGCCAAGAAACAAGTCTTGCCACAAGTTGCCGAAGAGTATATGCTCATGCACATGACTACCATATAAATTCGATATCAAATAACAG
upper sequence: GLYMA07G01440.1 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM2G164185_T02 (Zea mays), 3'ss of exon 5
--------------------------------------------------------------------------atttttgtatgtagtggagctag---------ttt--tcaagccttgacaattacttgtttgaa-----actttgtagtttagtgagtgctaacac--attgattgtaaa--atatgtagGTAACCAGCCATGAGACCAGTTTGGTGGCTCGATGTCGTAGAGTATATGCCCATGCTCATGATTATCATATTAATTCTATTTCAAATAACAG
||| || || | ||| |||| ||| | | || | ||| | ||| | | ||| | ||| | | | ||| | | | | |||| || |||| || ||||| || || ||| | | | | || || ||||||||||| ||||| ||||| || ||||| ||||| || |||||||||||
gtagttgtacttaactcagtttcatttatgcaccttgcaaaaccatattgtagttatttagaactattgagctgattcctggatattgtgtagctgaaaattgtattttagttgattctaaaatatttcctgtctatgtaaccattttttcttttcacaatttgttacattgactcagtataaactgtaaacagGTTACAAGCCAAGAAACAAGTCTTGCCACAAGTTGCCGAAGAGTATATGCTCATGCACATGACTACCATATAAATTCGATATCAAATAACAG
upper sequence: GLYMA07G01440.1 (Glycine max), 3'ss of exon 5
lower sequence: AT1G51690.3 (Arabidopsis thaliana), 3'ss of exon 7
-------atttttgtatgtagt--ggagctagttttcaagccttgacaattacttgtttgaaactttgtagtttagtgagtgctaacacattgattgtaaaatatgtagGTAACCAGCCATGAGACCAGTTTGGTGGCTCGATGTCGTAGAGTATATGCCCATGCTCATGATTATCATATTAATTCTATTTCAAATAACAG
| | | | ||| | || | ||| | || |||| || || | | || | ||| || | || |||| | | |||| ||||||| ||||||||| | || |||||| ||||||| ||||||||||| |||||||||||||||||||||||||| || |||||||||||
catggccttcactaccactgattaggaattgattcttaagtcatg-caata--ttacttaata-ttgctcatttgtagactaatagttcatt-----tgacatatacagGTAACTAGCCATGAGTCGAGCCCTGTGGCTAGATGTCGAAGAGTATATGCTCATGCTCATGATTATCATATTAATTCAATCTCAAATAACAG
upper sequence: GLYMA07G01440.1 (Glycine max), 3'ss of exon 5
lower sequence: AT1G17720.2 (Arabidopsis thaliana), 3'ss of exon 5
atttttgtatgtagtggagctagttttcaagccttgacaatt---acttgtttgaaactttgtagtttagtgagtgctaacacattgattgtaaaatatgtagGTAACCAGCCATGAGACCAGTTTGGTGGCTCGATGTCGTAGAGTATATGCCCATGCTCATGATTATCATATTAATTCTATTTCAAATAACAG
| ||| | | | | ||| ||| | | | | | | | | ||||| | || | | || | | || |||| ||||| |||||||| ||||| | | |||||| |||| || ||||| |||||||||||||||||||| ||||||||||| || || |||| |||
ttgtttccttttgtcgtaactaaagctcagtaccaaattagtctaatgcactagtcaatttgtgttctactt-gaacttatgggt--gtttctgcatatatagGTTACCAGCCAGGAGACTAACCTTGTGGCTAGATGCCGAAGAGTGTATGCCCATGCTCATGATTACCATATTAATTCAATCTCCAATAGCAG
upper sequence: GLYMA07G01440.1 (Glycine max), 3'ss of exon 5
lower sequence: Vv09s0002g02470.t01 (Vitis vinifera), 3'ss of exon 5
atttttgtatgtagtggagctagttttcaagcctt--gacaattacttgtttgaaactttgtagt---ttagtgagtgctaacacattgattgtaaaatatgtagGTAACCAGCCATGAGACCAGTTTGGTGGCTCGATGTCGTAGAGTATATGCCCATGCTCATGATTATCATATTAATTCTATTTCAAATAACAG
| || | ||||| | | | | | || ||| | || | || | | | || | ||||||| | | | || |||||||||||| | |||| ||||||||| |||||||| ||||||||||||| ||||| |||||||| || |||||||| ||||||||||||||||| ||
-----gttccaaggtatacttagttattacgtcattggatgtttaataagtttagtgttcatgataactgcctgtgatctaacacttccagtatacaatatgtagGTATCAAGCCCTGAGACCAGCCTGGTGGCTAGATGTCGTAGAGTTTATGCTCATGCTCACGACTATCATATCAATTCTATTTCAAATAATAGMapped 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|208080786|gb|GD875084.1|GD875084EST: ACGATTTCTCATTTCCACCAGAAGGCGTACCTTCTCTAAGATTACCATTG GTAACCAGCCATGAGACCAGTTTGGTGGCTCGATGTCGTAGAGTATATGCC
genomic: ACGATTTCTCATTTCCACCAGAAGGCGTACCTTCTCTAAGATTACCATTGgtagttgtgt ... aaatatgtagGTAACCAGCCATGAGACCAGTTTGGTGGCTCGATGTCGTAGAGTATATGCC
EST:
gi|22525826|gb|BU084637.1|BU084637EST: ACGATTTCTCATTTCCACCAGAAGGCGTACCTTCTCTAAGATTACCATTG GTAACCAGCCATGAGACCAGTTTGGTGGCTCGATGTCGTAGAGTATATGCC
genomic: ACGATTTCTCATTTCCACCAGAAGGCGTACCTTCTCTAAGATTACCATTGgtagttgtgt ... aaatatgtagGTAACCAGCCATGAGACCAGTTTGGTGGCTCGATGTCGTAGAGTATATGCC
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tgtttgaaactttgtagtttagtgagtgctaacacattgattgtaaaatatgtagGTAACCAGCCATGAGACCAGTTTGGTGGCTCGATGTCGTAGAGTATATGCCCATGCTCATGATTATCATATTAATTCTATTTCAAATAACAG
attgattgtaaaatat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
atttttgtatgtagtggagctagttttcaagccttgacaattacttgtttgaaactttgtagtttagtgagtgctaacacattgattgtaaaatatgtagGTAACCAGCCATGAGACCAGTTTGGTGGCTCGATGTCGTAGAGTATATGCCCATGCTCATGATTATCATATTAATTCTATTTCAAATAACAG
- - - - - gtagtgg
- - - - - - - - - - - - -ttcaagc
- - - - - - - - - - - - - - - - cttgaca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgagtgc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aacacat