Sequence
atgc intronic sequence ATGC exonic sequencegtttgtggactctacatgctagtttgagcatattttaggaaaccaccttttctacatgactattgtcgttaacctcattgtttgttgtagGTTCATTCGATCCGTGAGGCAGCTGCTAACAATTTGAAGCGCCTAGCTGAAGAATTTGGTCCTGAGTGGGCTATGCAACACATAATTCCACAG
Basic information
species | Glycine max |
transcript | GLYMA02G10790.1 |
intron # | 9 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA02G10790.1 (Glycine max), 3'ss of exon 9
lower sequence: LOC_Os09g07510.1 (Oryza sativa), 3'ss of exon 9
----gtttgtggactctacatgctagtttgagcatattttaggaaaccaccttttctacatgactatt------gtcgttaacctcattgtttgttgtagGTTCATTCGATCCGTGAGGCAGCTGCTAACAATTTGAAGCGCCTAGCTGAAGAATTTGGTCCTGAGTGGGCTATGCAACACATAATTCCACAG
||| || | || | | ||| | | | | || ||| || ||||| || ||||| || || || ||||| || ||| | || || ||||| ||||| ||||||||||||||||| || |||||||| || ||||| ||||| || ||||| || |||
ttgtgttcagtgattatatagtttttttttaatgcagaatggacaagtggtatttataacctgctatttaagatgtttttaactggatctttaattttagGTCTTCTCAATCAGAGATGCTGCTGCAAACAACTTGAAGCGCCTAGCTGAGGAGTTTGGTCCAGAATGGGCGATGCAGCATATAATCCCTCAG
upper sequence: GLYMA02G10790.1 (Glycine max), 3'ss of exon 9
lower sequence: GRMZM2G164352_T04 (Zea mays), 3'ss of exon 9
---------------------------------------------gtttgtggactctacatgcta---gtttgagcatattttaggaaaccaccttttctacatgactattgtc-gttaacctcattg---tttg--ttgtagGTTCATTCGATCCGTGAGGCAGCTGCTAACAATTTGAAGCGCCTAGCTGAAGAATTTGGTCCTGAGTGGGCTATGCAACACATAATTCCACAG
|| | | ||| || || ||||| || || ||| | | | | | |||||| ||| | || | | |||| || |||| ||| ||| | || || || |||||||| ||||||||||| || ||||| |||||||| |||||||| ||||| || ||||| || |||
gtttgtatcattagggttatgtcaaaacagtatctctttggagctgtctccagcgtctttatcttatatccttgagtgcatatt-ggactttgtaatgtattgactaaaattgtcagtttaactaactaaaatttggatttcagGTCTTTTCAATCAGAGATGCTGCCGCTAACAACTTGAAGCGCCTTGCAGAAGAGTTTGGTCCAGAGTGGGCAATGCAGCATATAATCCCTCAG
upper sequence: GLYMA02G10790.1 (Glycine max), 3'ss of exon 9
lower sequence: GRMZM2G102858_T01 (Zea mays), 3'ss of exon 9
---------------------------------------------------------gtttgtggactctac--atgctagtttgagcatattttag--gaaacc---accttttctacatgac----tattgtcgttaa---cctcattgtttgttgtagGTTCATTCGATCCGTGAGGCAGCTGCTAACAATTTGAAGCGCCTAGCTGAAGAATTTGGTCCTGAGTGGGCTATGCAACACATAATTCCACAG
| | |||| ||| | ||| || ||| | || ||| | | ||||| | | || || | || || | || | | ||||| |||||| | || || | ||| || ||||| ||||| | | || |||||||| ||||||||||| |||||||| |||||||| |||
gtgcataaataatttcaccaaccattattacacaagttccattaatgcagaaaccatgcatactatttctaatgatggtctttttagtctatataagttgaattcttgattgattctatgtaatgtaatagtgactcaaaataccaaacatttggcttcagGTTTTCTCGATCAGAGATGCTGGTGCCAATAATTTAAAGCGTTTGACAGAGGAATTTGGCCCTGAGTGGGCGATGCAACATATAATTCCTCAG
upper sequence: GLYMA02G10790.1 (Glycine max), 3'ss of exon 9
lower sequence: GRMZM2G122135_T04 (Zea mays), 3'ss of exon 9
----------------------------------------------------------gtttgtggactctacatgctagtttgagcatattttaggaaaccaccttttctacatgactattgtcgttaacctcattgtttgttgtagGTTCATTCGATCCGTGAGGCAGCTGCTAACAATTTGAAGCGCCTAGCTGAAGAATTTGGTCCTGAGTGGGCTATGCAACACATAATTCCACAG
| | | | || || | || ||| | || ||| | || | ||||| | | | || |||| || ||| | || || || || ||||| ||||||||||| || ||||| || ||||| |||||||| ||||| || |||||||| |||
gttcgtatcactagacttatgtcaaaacagtaacgctgtggggctactcaagcatctttcctttccatcttgtatcctcgagtgcatataggacattgtgatgtattgactaatggtttagattaactaaccaaaatttggatttcagGTCTTCTCAATCAGAGATGCTGCCGCCAACAACTTGAAGCGCCTTGCGGAAGAGTTCGGTCCAGAGTGGGCAATGCAGCATATAATTCCTCAG
upper sequence: GLYMA02G10790.1 (Glycine max), 3'ss of exon 9
lower sequence: AT1G13320.2 (Arabidopsis thaliana), 3'ss of exon 9
gtttgtggactctacatgctagtttgagcatattt-taggaaaccaccttttctacatgactattgtcgttaacctcattgtttgttgt-agGTTCATTCGATCCGTGAGGCAGCTGCTAACAATTTGAAGCGCCTAGCTGAAGAATTTGGTCCTGAGTGGGCTATGCAACACATAATTCCACAG
|| | | ||| | | || | ||| || || | ||| | || || | | ||| | |||| ||||||| || |||||||| || ||||| |||||| ||||||| || |||||||| ||||||||||| ||||| ||||| || ||| |||| |||
gtccctc-attctctaccttcattgaatcatccagataaataaatttgtcgtctctactgcttgaaattttgaaataattataaattgtcagGTTCACTCAATCCGTGAAGCTGCTGCAAACAATCTGAAGCGTCTTGCTGAAGAGTTTGGTCCTGAATGGGCAATGCAGCATATAGTTCCTCAG
upper sequence: GLYMA02G10790.1 (Glycine max), 3'ss of exon 9
lower sequence: AT3G25800.1 (Arabidopsis thaliana), 3'ss of exon 8
---------------------gtttgt--ggactctacatgctagtttgag-catattttaggaaaccaccttttctacatgactattgtcgttaacctcattgt------ttgttgtagGTTCATTCGATCCGTGAGGCAGCTGCTAACAATTTGAAGCGCCTAGCTGAAGAATTTGGTCCTGAGTGGGCTATGCAACACATAATTCCACAG
||| ||| | || || | | ||||| |||| |||| | | | || | || | ||| | |||||||| || ||||| || || |||||||||||| | ||||| || ||||| |||||||||||||| ||||| |||||||| ||| |||| |||
gtatttctttctctctcttacttttactgggaatgatcagattataccgcttcttatttatagaaattgatttttttttttttttttttttttttttttttttgcggatgctctcattagGTTCACTCAATCCGCGATGCTGCTGCTAACAATCTCAAGCGGCTTGCTGAGGAATTTGGTCCTGAATGGGCAATGCAACATATAGTTCCTCAG
upper sequence: GLYMA02G10790.1 (Glycine max), 3'ss of exon 9
lower sequence: Vv01s0011g03280.t01 (Vitis vinifera), 3'ss of exon 8
----gtttgtggactctacatgctagtttgagcatatt-ttaggaaaccaccttt---tctacatgact--attgtcgttaacctcattgtttgttgtagGTTCATTCGATCCGTGAGGCAGCTGCTAACAATTTGAAGCGCCTAGCTGAAGAATTTGGTCCTGAGTGGGCTATGCAACACATAATTCCACAG
| | || || | | | | | | || || | || || | | || | | | | || | || | | || ||||| | || || ||||| || ||||||||||| || |||||||| || ||||||||||||||||| ||||| ||||| ||| |||||||||||
tattttaagagggctttcatcatctttgtcatcgttttctttgtctgtcatctatgtatttatgtagttcaaaagggacaaatattatcatgttgtgcagGTTTACTCCATTCGTGATGCTGCTGCTAACAACTTAAAGCGCCTTGCAGAAGAATTTGGTCCTGACTGGGCAATGCAGCACTTAATTCCACAG
upper sequence: GLYMA02G10790.1 (Glycine max), 3'ss of exon 9
lower sequence: PP1S214_34V6.1 (Physcomitrella patens), 3'ss of exon 8
------------------------------------gtttgtggactctacatgctagt--ttgagcatattttaggaaaccaccttttctacatgactattgtcgt----taacctcattgtttgttg------tagGTTCATTCGATCCGTGAGGCAGCTGCTAACAATTTGAAGCGCCTAGCTGAAGAATTTGGTCCTGAGTGGGCTATGCAACACATAATTCCACAG
||||||| || | ||| | || | | || || | | |||| | |||| | || ||| ||||| ||| ||| ||||| | || ||||| ||||||||||| |||||| | ||||| || || ||||| ||||||||||||||||| |||| ||||| |||||||||
gttcatatattcccatcaagcaatgtttcgatggtggtttgtg---tcgagatggtcgtcctcaatcagatctcttttcatatttgcttctttagaactagttcagtaatataatttcattcttttttggattaatagGTGTACTCTATCCGAGAGGCAGCTGCCAACAATCTCAAGCGTCTTGCCGAAGAGTTTGGTCCTGAGTGGGCATTGCAGCACATCATTCCACAGMapped 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|15202124|gb|BI425235.1|BI425235EST: TGCATGCAGTGGTTACAGGACAAG GTTCATTCGATCCGTGAGGCAGCTGCTAACAATTTGAAGCGCCTAGCTGAA
genomic: TGCATGCAGTGGTTACAGGACAAGgtttgtggac ... tttgttgtagGTTCATTCGATCCGTGAGGCAGCTGCTAACAATTTGAAGCGCCTAGCTGAA
EST:
gi|58015550|gb|CX702292.1|CX702292EST: TTTGCATGCAGTGGTTACAGGACAAG GTTCA-TCGATTCCGTGAGGCAGCTGCTAACAATTTGAAGCGCCTAGCTGA
genomic: TTTGCATGCAGTGGTTACAGGACAAGgtttgtggac ... tttgttgtagGTTCATTCGA-TCCGTGAGGCAGCTGCTAACAATTTGAAGCGCCTAGCTGA
EST:
gi|6666156|gb|AW277615.1|AW277615EST: NNNNNNATGACAAACTTGGTGCTCTTTGCATGCAGTGGTTACAGGACAAG GTTCATTCGATCCGTGAGGCAGCTGCTAACAATTTGAAGCGCCTAGCTGAA
genomic: TTTTTTATGACAAACTTGGTGCTCTTTGCATGCAGTGGTTACAGGACAAGgtttgtggac ... tttgttgtagGTTCATTCGATCCGTGAGGCAGCTGCTAACAATTTGAAGCGCCTAGCTGAA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.taggaaaccaccttttctacatgactattgtcgttaacctcattgtttgttgtagGTTCATTCGATCCGTGAGGCAGCTGCTAACAATTTGAAGCGCCTAGCTGAAGAATTTGGTCCTGAGTGGGCTATGCAACACATAATTCCACAG
cgttaac putative branch site (score: 3)
ttttcta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtttgtggactctacatgctagtttgagcatattttaggaaaccaccttttctacatgactattgtcgttaacctcattgtttgttgtagGTTCATTCGATCCGTGAGGCAGCTGCTAACAATTTGAAGCGCCTAGCTGAAGAATTTGGTCCTGAGTGGGCTATGCAACACATAATTCCACAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA