Sequence
atgc intronic sequence ATGC exonic sequencegtatgagctctaccttagtttgttgctcttcttattaagttcttaatcagtgcggtggcattgtccaaaggttcttatcaaattattgggtcattttgtccacttggctaaccatataaacatgatgtaagaattgtaatgtggggtttcattttgttgtggcagTTGATTGTGCTTTATGTGGTTTTCAAGCTTGACGAGAGTTACACGCCGAGCAAAGTTTCCATCCTTGCCGGTGATGGTTTTCACAACTTGAAGGTAAATT
Basic information
species | Glycine max |
transcript | GLYMA20G20840.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA20G20840.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G054247_T04 (Zea mays), 3'ss of exon 2
gtatgagctctaccttagtttgttgctcttcttattaagttcttaatcagtgcggtggcattgtccaaaggttcttatcaaattattgggtcattttgtccacttggctaaccatataaacatgatgtaagaattgtaatgtggggtttcattttgttgtggcagTTGATTGTGCTTTATGTGGTTTTCAAGCTTGACGAGAGTTACACGCCGAGCAAAGTTTCCATCCTTGCCGGTGATGGTTTTCACAACTTGAAGGTAAATT
|| | | | || | || | | ||| || || | || | | | | ||| |||| || |||| | || || | ||||||| || |||| ||||||||| ||||||||||||||||||||||| | ||||||| ||||| ||||| || |||||| | |||||| |
----------------------------------------------------------------------gtgcctgcttcagtagag----atgctactcctttgccttgtgattcga---tggttttgagact--aatt---ggttctatgttgt-gcggtagCTCGTTGTGCTCTACGTGGATTTCAAGCTCGACGAGAGTTACACGCCGAGCAAGATCTCCATCCGGGCCGGGGATGGCTTCCACAACCTAAAGGTACGCT
upper sequence: GLYMA20G20840.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G054247_T03 (Zea mays), 3'ss of exon 2
gtatgagctctaccttagtttgttgctcttcttattaagttcttaatcagtgcggtggcattgtccaaaggttcttatcaaattattgggtcattttgtccacttggctaaccatataaacatgatgtaagaattgtaatgtggggtttcattttgttgtggcagTTGATTGTGCTTTATGTGGTTTTCAAGCTTGACGAGAGTTACACGCCGAGCAAAGTTTCCATCCTTGCCGGTGATGGTTTTCACAACTTGAAGGTAAATT
|| | | | || | || | | ||| || || | || | | | | ||| |||| || |||| | || || | ||||||| || |||| ||||||||| ||||||||||||||||||||||| | ||||||| ||||| ||||| || |||||| | |||
----------------------------------------------------------------------gtgcctgcttcagtagag----atgctactcctttgccttgtgattcga---tggttttgagact--aatt---ggttctatgttgt-gcggtagCTCGTTGTGCTCTACGTGGATTTCAAGCTCGACGAGAGTTACACGCCGAGCAAGATCTCCATCCGGGCCGGGGATGGCTTCCACAACCTAAAG-------
upper sequence: GLYMA20G20840.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv04s0023g01940.t01 (Vitis vinifera), 3'ss of exon 2
gtatgagctctaccttagtttgttgctcttcttattaagttcttaatcagtgcggtggcattgtccaaaggttcttatcaaattattgggtcattttgtccacttggctaaccatataaacatgatgtaagaattgtaatgtggggtttcattttgttgtggcagTTGATTGTGCTTTATGTGGTTTTCAAGCTTGACGAGAGTTACACGCCGAGCAAAGTTTCCATCCTTGCCGGTGATGGTTTTCACAACTTGAAGGTAAATT
|| | | || | || || | ||| | | | || | | | | || || |||| || | | |||| || || || |||| ||||||||| ||||||||| |||||||| ||||||||||| || | || || | ||||| ||||| || ||||||||||||
--------------------------------------------------------------gtgtgtatgcaatt-ttgggtttctgatttttttctttcccc---cttatcgtttggttttggtgactgaatggtgaa--tagatttctcttaa-------agCTGGTTGTAATTTATGTGGATTTCAAGCTGGACGAGAGCTACACGCCGAGTAAGATCTCTATTCGAGCCGGAGATGGCTTCCACAACTTGAAG------- atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.accatataaacatgatgtaagaattgtaatgtggggtttcattttgttgtggcagTTGATTGTGCTTTATGTGGTTTTCAAGCTTGACGAGAGTTACACGCCGAGCAAAGTTTCCATCCTTGCCGGTGATGGTTTTCACAACTTGAAGGTAAATT
ggctaac putative branch site (score: 2)
ttttgtt putative PPT
aattgtaat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatgagctctaccttagtttgttgctcttcttattaagttcttaatcagtgcggtggcattgtccaaaggttcttatcaaattattgggtcattttgtccacttggctaaccatataaacatgatgtaagaattgtaatgtggggtttcattttgttgtggcagTTGATTGTGCTTTATGTGGTTTTCAAGCTTGACGAGAGTTACACGCCGAGCAAAGTTTCCATCCTTGCCGGTGATGGTTTTCACAACTTGAAGGTAAATT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG