Sequence
atgc intronic sequence ATGC exonic sequencegtacttttactttaacttaatcatatttttatcttcattttgccataaaaagtgttaagaattttgtgttgtaaaagattctttttgagtttgattgctaatataatgcaatgtgtttgaaccaccatacagCCACATTCCCCCGATAATCGTGCTTTGGCAAGAGAATGCAACAATGTGAAAATTGACAGAGTATACATTGGATCCTGCACTGGTGGGAAGACTGAAGATT
Basic information
species | Glycine max |
transcript | GLYMA20G34160.1 |
intron # | 13 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA20G34160.1 (Glycine max), 3'ss of exon 13
lower sequence: GRMZM2G370852_T02 (Zea mays), 3'ss of exon 10
gtacttttactttaacttaatcatatttttatcttcattttgccataaaaagtgttaa--gaattttgtgttgtaaaagattctttttgagtttgattgctaatataatgcaatgtgtttgaaccaccatacagCCACATTCCCCCGATAATCGTGCTTTGGCAAGAGAATGCAACAATGTGAAAATTGACAGAGTATACATTGGATCCTGCACTGGTGGGAAGACTGAAGATT
|||| | | | || |||| | | | ||| ||| | || | | ||||| | | | | ||||||||||| || || || ||||| | |||||||||||||| |||| || || ||| |||| || ||||| |||||||||||||| |||||||| || |
-------------------------------------------------gtctgttgatgtagtattttgttatcttcatcttctgttgcttttc-ctataaaaacgaagcaataactgcctttgatc-tgcagCCACATTCGCCTGACAACCGTGCCCTAGCAAGAGAATGCAAAGATGTCAAGATCGACCGAGTCTATATTGGTTCCTGCACTGGTGGCAAGACTGAGGACT
upper sequence: GLYMA20G34160.1 (Glycine max), 3'ss of exon 13
lower sequence: GRMZM2G010044_T01 (Zea mays), 3'ss of exon 10
gtacttttactttaacttaatcatatttttatcttcattttgccataaaaagtgttaa-gaattttgtgttgtaa--aagattctttttgagtttgattgctaatataatgcaatgtgtttgaaccaccatacagCCACATTCCCCCGATAATCGTGCTTTGGCAAGAGAATGCAACAATGTGAAAATTGACAGAGTATACATTGGATCCTGCACTGGTGGGAAGACTGAAGATT
|||| | ||| | | || || | || ||| | |||| | || | || | ||| | | ||| | ||||||||||| || || || |||||| |||||||||||||| ||||||| || ||| |||| || ||||| || ||||||||||| ||||| || ||||
-------------------------------------------------gtttgttggcgcattattttctgcaatcgacatcttttgttggttttcctataaaaacaaaggaatacctgtcttggacc-tgcagCCACATTCGCCTGACAACCGTGCTCCAGCAAGAGAATGCAAAGATGTGAAGATCGACCGAGTCTATATTGGTTCTTGCACTGGTGGTAAGACCGAGGATT
upper sequence: GLYMA20G34160.1 (Glycine max), 3'ss of exon 13
lower sequence: AT4G13430.1 (Arabidopsis thaliana), 3'ss of exon 11
gtacttttactttaacttaatcatatttttatcttcattttgccataaaaagtgttaagaattttgtgttgtaaaagattctttttgagtttgattgctaatataatgcaatgtgtttgaaccaccatacagCCACATTCCCCCGATAATCGTGCTTTGGCAAGAGAATGCAACAATGTGAAAATTGACAGAGTATACATTGGATCCTGCACTGGTGGGAAGACTGAAGATT
|| | | | | || ||| | | ||| | | | || || || | | ||||| ||| | ||||| ||||| || || || || ||| | || ||||||||||| | ||||||||||||||||||||||| || || || |||||||||||||| || ||||
---------------------------------------gtgggtttacgattaccaa----tttaaacactgagttatttctgccacttcaggttacttattttgt-taatgtcttt------tttttcagCCTCATTCTCCTGACAACCGAGCTCTAGCTAGAGAATGCAAAGACGTGAAAATTGACAGAGTATACATCGGTTCTTGTACTGGTGGGAAGACAGAGGATT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.attctttttgagtttgattgctaatataatgcaatgtgtttgaaccaccatacagCCACATTCCCCCGATAATCGTGCTTTGGCAAGAGAATGCAACAATGTGAAAATTGACAGAGTATACATTGGATCCTGCACTGGTGGGAAGACTGAAGATT
tgctaat putative branch site (score: 2)
attgctaatataat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtacttttactttaacttaatcatatttttatcttcattttgccataaaaagtgttaagaattttgtgttgtaaaagattctttttgagtttgattgctaatataatgcaatgtgtttgaaccaccatacagCCACATTCCCCCGATAATCGTGCTTTGGCAAGAGAATGCAACAATGTGAAAATTGACAGAGTATACATTGGATCCTGCACTGGTGGGAAGACTGAAGATT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA