Sequence
atgc intronic sequence ATGC exonic sequence...tcttgaccgtattcactcttatgcttttctctaggtgcattgttgttgttctttacttgtctcattgtttactaactatttttaagctgttttcatgcagTTGATATACAGACCTGACACTGGAGAGATATTGGGAGTCCATATATTTGGGTTGCATGCTGCTGATCTCATCCACGAGGCATCCAATGCAATAGCACTAG
Basic information
species | Glycine max |
transcript | GLYMA09G04270.1 |
intron # | 7 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA09G04270.1 (Glycine max), 3'ss of exon 7
lower sequence: LOC_Os01g23610.1 (Oryza sativa), 3'ss of exon 12
-----------------------------------------------tcttgaccgtattc-actcttatgctt--ttctctaggtgcattgttgtt------gttctttacttgtctcattgtttactaactatttttaagctgt---tttcatgcagTTGATATACAGACCTGACACTGGAGAGATATTGGGAGTCCATATATTTGGGTTGCATGCTGCTGATCTCATCCACGAGGCATCCAATGCAATAGCACTAG
| | | | ||| | ||| | | || ||| | | || | | | || | | | | | | | | | || | ||| | ||| |||| ||| | |||||||||||||| || | ||||| || ||||| || |||||||||||||| ||||||||||||||||| || || || || || |
gtgattctacttttccaccttattgtattctagacctaaactgtttcttataatcacattggatccttgcaatgaatactgtagtcagactaatgctaaagaggaaatctatccttggaacttgaaaatgatgagacatgaactctacttttgctacagATGATTTACCGGCCTGACACTGGAGAAATTCTTGGAGTTCACATATTAGGTTTGCATGCTGCTGACCTCATCCACGAGGCATCAAACGCCATTGCCCTCG
upper sequence: GLYMA09G04270.1 (Glycine max), 3'ss of exon 7
lower sequence: LOC_Os05g06460.1 (Oryza sativa), 3'ss of exon 12
-------------------------------------------------------------------------tcttgacc-gtattcactcttatgcttttctctaggtgcattgttgttgttctttacttgtctcattgtttactaactatttttaagctgttttcatgcagTTGATATACAGACCTGACACTGGAGAGATATTGGGAGTCCATATATTTGGGTTGCATGCTGCTGATCTCATCCACGAGGCATCCAATGCAATAGCACTAG
| ||| | || | || | | | | | | || ||| ||| || || | | | | || | || || | | |||| |||||||||| ||| | |||||||||||||| || | || || || || || || ||||| |||||||| ||||||||||||||||| ||||| || || ||||
gtatacatgtttttagtttgtgccacttatttctatcagttttttttccttgcagggttatttctatcagttgtgttgtcttgtctccaaattggcacctgggtattgctgtcttgcatggcttcattcagtgacatactttgggcttgacaattgtatgttcctttc-tgcagTTGATTTACCGGCCTGACACTGGAGAAATTCTTGGTGTGCACATTTTGGGTTTGCACGCTGCTGACCTCATCCACGAGGCATCAAATGCCATTGCCCTAG
upper sequence: GLYMA09G04270.1 (Glycine max), 3'ss of exon 7
lower sequence: GRMZM2G145595_T01 (Zea mays), 3'ss of exon 12
--------------------------------------------------------tcttgaccgtattcactcttatgcttttctctaggtgcattgttgttgttctttacttgtctcattgtttactaactatttttaagctgttttcatgcagTTGATATACAGACCTGACACTGGAGAGATATTGGGAGTCCATATATTTGGGTTGCATGCTGCTGATCTCATCCACGAGGCATCCAATGCAATAGCACTAG
| | | || || | | | ||||| ||| | | | ||| | | | | | || || | || |||| ||| |||| || | |||||||| ||||| || | ||||| ||||| || || ||||||||||||||||||||||| |||||||| ||||| || || || |
gtagtaatgcggtagtgtgtttccaccctgttgcattctaaatttatgcacggagaattccagtggatacattaaccagacctatgctagggagcctgt----atccatggaacctctaaatttgaagtgacgatacatgtactattttgcctcagATGATTTATCGCCCTGACACCGGAGAAATTCTTGGAGTTCATATTTTGGGCTTGCATGCTGCTGATCTCATCCATGAGGCATCAAATGCCATTGCCCTTG
upper sequence: GLYMA09G04270.1 (Glycine max), 3'ss of exon 7
lower sequence: GRMZM2G073774_T01 (Zea mays), 3'ss of exon 12
----tcttgaccgta--ttcactcttatgcttttctctaggtgcattgttgttgttctttacttgtctcattgtttactaactatttttaagctgttttca-tgcagTTGATATACAGACCTGACACTGGAGAGATATTGGGAGTCCATATATTTGGGTTGCATGCTGCTGATCTCATCCACGAGGCATCCAATGCAATAGCACTAG
| || | ||||| | ||| ||| | | | |||| || | | | | ||||| | | | || | || ||| |||||||||| ||| |||||||||| || || || | || || || || || || |||||||||||||||||||| ||||||||||| ||||| || || ||||
gtcattctgtttgctacttcacgttcatgttttctccagaatttacacatgttctttgtcaagt-tttcattaac-agaatttgacaatatgtggtcctcactgcagTTGATTTACCGACCTGACACGGGTGAAATTCTTGGGGTTCACATTTTGGGTTTGCATGCTGCTGATCTCATTCACGAGGCATCAAATGCCATCGCCCTAG
upper sequence: GLYMA09G04270.1 (Glycine max), 3'ss of exon 7
lower sequence: GRMZM2G152958_T02 (Zea mays), 3'ss of exon 12
----tcttgaccgta--ttcactcttatgcttttctctaggtgcattgttgttgttctttacttgtctcattgtttactaactatttttaagctgttttca-tgcagTTGATATACAGACCTGACACTGGAGAGATATTGGGAGTCCATATATTTGGGTTGCATGCTGCTGATCTCATCCACGAGGCATCCAATGCAATAGCACTAG
| || | ||||| | ||| ||| | | | |||| || | | | | ||||| | | | || | || ||| |||||||||| ||| |||||||||| || || || | || || || || || || |||||||||||||||||||| ||||||||||| |
gtcattctgtttgctacttcacgttcatgttttctccagaatttacacatgttctttgtcaagt-tttcattaac-agaatttgacaatatgtggtcctcactgcagTTGATTTACCGACCTGACACGGGTGAAATTCTTGGGGTTCACATTTTGGGTTTGCATGCTGCTGATCTCATTCACGAGGCATCAA---------------
upper sequence: GLYMA09G04270.1 (Glycine max), 3'ss of exon 7
lower sequence: AT4G16155.1 (Arabidopsis thaliana), 3'ss of exon 12
tcttgaccgtattcactcttatgcttttctctaggtgcattgttgt---tgttctttacttgtctcattgtttactaactatttttaagctgttttcatg----cagTTGATATACAGACCTGACACTGGAGAGATATTGGGAGTCCATATATTTGGGTTGCATGCTGCTGATCTCATCCACGAGGCATCCAATGCAATAGCACTAG
||| | || | | | | | || ||||| | | | || || | | | ||| | | || | |||||| ||| |||||||||||||||||| ||| || || | ||||| ||||||||||| ||||||||||||||||| ||||| || ||||| || || || || |||
--gtgaagagaagaac-caaaaattgaaataaaaaaagatagttgtatatagttctggagtgacttgc-gaagataagatatctgaacactctcttcatgtgaacagATGATATACAGACCTGACAATGGTGAAATCCTTGGAGTTCATATATTTGGATTGCATGCTGCTGATCTTATCCATGAAGCATCAAACGCGATTGCTTTAG
upper sequence: GLYMA09G04270.1 (Glycine max), 3'ss of exon 7
lower sequence: AT3G16950.2 (Arabidopsis thaliana), 3'ss of exon 12
tcttgaccgtattcactcttatgcttttctctaggtgcatt-gttgttgttctttacttgtctcattgtttac--taactatttttaagctgttt-tcatgcagTTGATATACAGACCTGACACTGGAGAGATATTGGGAGTCCATATATTTGGGTTGCATGCTGCTGATCTCATCCACGAGGCATCCAATGCAATAGCACTAG
|| ||| ||||||| | | | |||||||| | || || | ||| || | |||||| |||||||| ||||||||| ||| || || || ||||| ||||||||||| ||||||| ||||| || ||||| || || || ||||| || || ||||
---------------------------gtgggagaagcaaaagttgttgatttatttatgtctcatgaaagaacatagagatctcattgcttttcattatgcagATGATATACCGACCTGACAATGGTGAAATCTTAGGAGTTCATATATTTGGACTGCATGCAGCTGACCTTATCCATGAAGCTTCTAATGCGATTGCTCTAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttgttctttacttgtctcattgtttactaactatttttaagctgttttcatgcagTTGATATACAGACCTGACACTGGAGAGATATTGGGAGTCCATATATTTGGGTTGCATGCTGCTGATCTCATCCACGAGGCATCCAATGCAATAGCACTAG
tactaac putative branch site (score: 0)
ctgttttc putative PPT
attgtttactaactat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tcttgaccgtattcactcttatgcttttctctaggtgcattgttgttgttctttacttgtctcattgtttactaactatttttaagctgttttcatgcagTTGATATACAGACCTGACACTGGAGAGATATTGGGAGTCCATATATTTGGGTTGCATGCTGCTGATCTCATCCACGAGGCATCCAATGCAATAGCACTAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT
-cttgacc
- - - - - - - - -cttatgc
- - - - - - - - - - - - - - - - aggtgca
- - - - - - - - - - - - - - - - - - - - -gttgttg