Sequence
atgc intronic sequence ATGC exonic sequence...gtcacaagacttgttctgcgctctcattttctttgggttcatttactactctgtttttaccagcttgacattactaattgtcgtttatgctttcttgcagTTGATATACAGACCTGACAATGGAGAGATACTAGGAGTTCATATTTTTGGTTTGCATGCAGCAGATCTCATCCATGAAGCATCCAATGCAATAGCATTAG
Basic information
species | Glycine max |
transcript | GLYMA17G03560.1 |
intron # | 12 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA17G03560.1 (Glycine max), 3'ss of exon 12
lower sequence: GRMZM2G145595_T01 (Zea mays), 3'ss of exon 12
-----------------------------gtcacaagacttgttc-tgcgctctcattttctttgggttcatttacta---ctctgtt--------tttacc-----agcttgacattactaattgtcgtt---tatgctttcttg---cagTTGATATACAGACCTGACAATGGAGAGATACTAGGAGTTCATATTTTTGGTTTGCATGCAGCAGATCTCATCCATGAAGCATCCAATGCAATAGCATTAG
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gtagtaatgcggtagtgtgtttccaccctgttgcattctaaatttatgcacggagaattccagtggatacattaaccagacctatgctagggagcctgtatccatggaacctctaaatttgaagtgacgatacatgtactattttgcctcagATGATTTATCGCCCTGACACCGGAGAAATTCTTGGAGTTCATATTTTGGGCTTGCATGCTGCTGATCTCATCCATGAGGCATCAAATGCCATTGCCCTTG
upper sequence: GLYMA17G03560.1 (Glycine max), 3'ss of exon 12
lower sequence: GRMZM2G073774_T01 (Zea mays), 3'ss of exon 12
gtcacaagacttgtt---ctgcgctctcattttcttt-gggttcatttac-tactctgtttttaccagcttgacattactaattgtcgtttatgctttcttgcagTTGATATACAGACCTGACAATGGAGAGATACTAGGAGTTCATATTTTTGGTTTGCATGCAGCAGATCTCATCCATGAAGCATCCAATGCAATAGCATTAG
|||| ||| | || || |||||| | || | | | || ||| || ||| | | | | | | |||||||||| ||| ||||||||| || || || || || ||||| ||||| ||||||||||| || |||||||| || || ||||| ||||| || || |||
gtcattctgtttgctacttcacgttcatgttttctccagaatttacacatgttctttgtcaagttttcattaacagaatttgacaatatgtggtcctcactgcagTTGATTTACCGACCTGACACGGGTGAAATTCTTGGGGTTCACATTTTGGGTTTGCATGCTGCTGATCTCATTCACGAGGCATCAAATGCCATCGCCCTAG
upper sequence: GLYMA17G03560.1 (Glycine max), 3'ss of exon 12
lower sequence: AT4G16155.1 (Arabidopsis thaliana), 3'ss of exon 12
---gtcacaagacttgttctgcgctctcattttctttgggttcatttactactctgtt--tttaccagcttgacattactaattgtcgtttatgctttcttgcagTTGATATACAGACCTGACAATGGAGAGATACTAGGAGTTCATATTTTTGGTTTGCATGCAGCAGATCTCATCCATGAAGCATCCAATGCAATAGCATTAG
| |||| | | | | | | || || | || | || | | | | || || | | | | | | ||| |||||||||||||||||||||| || || || ||||||||||| ||||| |||||||| || ||||| |||||||||||||| || || || || ||||
gtgaagagaagaaccaaaaattgaaataaaaaaagatagttgtatatagttctggagtgacttgcgaagataagatatctgaacac--tctcttcatgtgaacagATGATATACAGACCTGACAATGGTGAAATCCTTGGAGTTCATATATTTGGATTGCATGCTGCTGATCTTATCCATGAAGCATCAAACGCGATTGCTTTAG
upper sequence: GLYMA17G03560.1 (Glycine max), 3'ss of exon 12
lower sequence: AT3G16950.2 (Arabidopsis thaliana), 3'ss of exon 12
gtcacaagacttgttctgcgctctcattttctttgggttcatttactactctgtttttaccagcttgacattactaattgtcgtttatgctttcttgcagTTGATATACAGACCTGACAATGGAGAGATACTAGGAGTTCATATTTTTGGTTTGCATGCAGCAGATCTCATCCATGAAGCATCCAATGCAATAGCATTAG
|| | | || || | || ||||| ||| | | | | || || || |||| || || ||||| |||||||| ||||||||||||| || || ||||||||||||| ||||| |||||||||| || || ||||||||||| || ||||| || || |||
------------gtgggagaagcaaaagttgtt--gatttatttat--gtctcatgaaagaacatagagat--ctcattgcttttcat-----tatgcagATGATATACCGACCTGACAATGGTGAAATCTTAGGAGTTCATATATTTGGACTGCATGCAGCTGACCTTATCCATGAAGCTTCTAATGCGATTGCTCTAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ctactctgtttttaccagcttgacattactaattgtcgtttatgctttcttgcagTTGATATACAGACCTGACAATGGAGAGATACTAGGAGTTCATATTTTTGGTTTGCATGCAGCAGATCTCATCCATGAAGCATCCAATGCAATAGCATTAG
tactaat putative branch site (score: 1)
tgctttctt putative PPT
attactaatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtcacaagacttgttctgcgctctcattttctttgggttcatttactactctgtttttaccagcttgacattactaattgtcgtttatgctttcttgcagTTGATATACAGACCTGACAATGGAGAGATACTAGGAGTTCATATTTTTGGTTTGCATGCAGCAGATCTCATCCATGAAGCATCCAATGCAATAGCATTAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC
- - - - -cttgttc
- - - - - - - - - cgctctc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gcttgac
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tttatgc