Sequence
atgc intronic sequence ATGC exonic sequencegtaatggtcaactctcaactcctgaaacagtagttttttttgaatacagcctacattctttcattgttatttttgcttaataaattgtatgttgctgctgctttagGGATTTGAAGCACGAGGAGAAGCGTTGTGTGGAGGAGCTTCAGTGCAACATTGTTGTTATGAAGCGTTCTCAGCCTAAAGTCCTTCGGCTTAATCTTGTG
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GRMZM2G057618_T02 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os01g41870.1 (Oryza sativa), 3'ss of exon 4
gtaatggtcaactctcaactcctgaaacagtagttttttttgaatacagcctacattctttcattgttatttttgcttaataaattgtatgttgctgctgctttagGGATTTGAAGCACGAGGAGAAGCGTTGTGTGGAGGAGCTTCAGTGCAACATTGTTGTTATGAAGCGTTCTCAGCCTAAAGTCCTTCGGCTTAATCTTGTG
|| |||| |||| ||||| | | |||||| | || | ||| || | |||| || || ||||| ||||| || ||||| |||||||| || ||||| | ||| ||||||||||| ||||| || ||||||||||||||||||||||| |||||||| ||||| | |||||||||
-------gtaagggtcaaatcctattacagtg----tgcataaatacatcataaccttttttttttctgttttct-----tatgtttcatgtttctgctaatt-agGGAGTTGAAGCATGAAGAGAAACATTGCGTGGAGGAGCTACAGTGTAATATTGTTGTTATGAAGCGTTCTCAACCTAAAGTTGTTCGGTTGAATCTTGTG
upper sequence: GRMZM2G057618_T02 (Zea mays), 3'ss of exon 4
lower sequence: GLYMA08G20750.1 (Glycine max), 3'ss of exon 3
gtaatggtcaactctcaact--cctgaaacagtagtttttt---------------ttgaatacagcctacattctttcattgttatttttgcttaa---taaattgtatgttgctgctgcttt---agGGATTTGAAGCACGAGGAGAAGCGTTGTGTGGAGGAGCTTCAGTGCAACATTGTTGTTATGAAGCGTTCTCAGCCTAAAGTCCTTCGGCTTAATCTTGTG
||||| ||| | | | ||| | || || || | | || ||||||| || || || ||| | | |||||| | ||||| ||| || || | | || || ||||| ||||| || |||| || || ||||| |||||||| |||||||||||||||||||||||||| || || | ||| | |
gtaatagtctctcttatattttcctcactgagaagcttcctattgtaaccataaaacttgatgatatctacatttttggtttattgtttcgttctgagattaaattttgtgttgttgccttctttgcagACAGCTTAAACATGAGGAAAAGCGATGCATGGAAGAACTGCAGTGTAACATTGTAGTTATGAAGCGTTCTCAGCCTAAAGTACTGCGCTTGAATTTGATT
upper sequence: GRMZM2G057618_T02 (Zea mays), 3'ss of exon 4
lower sequence: GLYMA07G01350.1 (Glycine max), 3'ss of exon 3
gtaatggtc----aactctcaa---ctcctga--aacagtagttttttttgaatacagcctacattctttcattgttatttt--tgctta------------ataaattgtatgttgctg----------ctgcttt------agGGATTTGAAGCACGAGGAGAAGCGTTGTGTGGAGGAGCTTCAGTGCAACATTGTTGTTATGAAGCGTTCTCAGCCTAAAGTCCTTCGGCTTAATCTTGTG
||||| ||| | |||| | |||| | | || | | ||||| || | || |||| || || || |||| || ||| || | | | ||||| || ||| || || | | || || ||||| ||||| || |||| || || ||||| |||||||| ||||||||||||||||| |||||||| || || | ||| | |
gtaatagtctctcagctcttatattttcctcactgatagacatgctatttgattata-tctccatttttgacttattgttttgttgtttacctgagattataattgagtttgtgttgttggcttttggtgttgccttttttgcagACAGCTCAAACATGAGGAAAAGCGATGCATGGAAGAACTGCAGTGTAACATTGTGGTTATGAAGCGTTCTCAACCTAAAGTACTGCGCTTGAATTTGATT
upper sequence: GRMZM2G057618_T02 (Zea mays), 3'ss of exon 4
lower sequence: Vv09s0002g02420.t01 (Vitis vinifera), 3'ss of exon 3
---------------------------------------------------------------gtaatggtcaactctcaactcctg----aaacagtagttt-----tttttgaatacagcctacattctttcattgttatttttgcttaataaattgtatgttgctgctgcttt----agGGATTTGAAGCACGAGGAGAAGCGTTGTGTGGAGGAGCTTCAGTGCAACATTGTTGTTATGAAGCGTTCTCAGCCTAAAGTCCTTCGGCTTAATCTTGTG
| ||| | || | | || || | || || | ||| | | |||| || | ||| | ||| | | | || | ||| || || | | ||| | | || || ||||| || | || |||||||||| || ||||||||||| ||||||||||| || || |||||||| || || | ||| | ||
gtaatatactctttctaatttttccataaaaatgtttttatttatttatttattttcatttccctcctgggaattcctttatttctctgtcaagctgttgtctattaatttcttggttcagcagttatgtccttattttcattactcttcccttggttaaaagttacttgtgttatgtgcagGCAGCTCAAACATGAGGAAAAATGCTGCATGGAGGAGCTGCAATGCAACATTGTGGTTATGAAGCGCTCCCAACCTAAAGTTCTCCGCTTGAATTTGGTT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tacattctttcattgttatttttgcttaataaattgtatgttgctgctgctttagGGATTTGAAGCACGAGGAGAAGCGTTGTGTGGAGGAGCTTCAGTGCAACATTGTTGTTATGAAGCGTTCTCAGCCTAAAGTCCTTCGGCTTAATCTTGTG
gcttaat putative branch site (score: 4)
ctgcttt putative PPT
tttcattgttattttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaatggtcaactctcaactcctgaaacagtagttttttttgaatacagcctacattctttcattgttatttttgcttaataaattgtatgttgctgctgctttagGGATTTGAAGCACGAGGAGAAGCGTTGTGTGGAGGAGCTTCAGTGCAACATTGTTGTTATGAAGCGTTCTCAGCCTAAAGTCCTTCGGCTTAATCTTGTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC