Sequence
atgc intronic sequence ATGC exonic sequence...cacttatatttttttgcgggcaaattgccagctactgactggcttctaatgataaagtttttgaaaaatcttccttttccaattcttttttctagagtagTGATGCTGAGGAAGGTAAGTCCAAGAAGGGTCAATATGAAGGGCCAGATATGGACTTAGCTGCAATGCTTGAAAGGGATGTTCTGGATTCTACTCCAGGA
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GRMZM2G054715_T02 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os01g49000.1 (Oryza sativa), 3'ss of exon 2
--cacttatatt-tttttgcgggcaaattgccagctactgactggcttctaatgataaagtttttgaaaaatctt-ccttttccaattcttttttc-tagagtagTGATGCTGAGGAAGGTAAGTCCAAGAAGGGTCAATATGAAGGGCCAGATATGGACTTAGCTGCAATGCTTGAAAGGGATGTTCTGGATTCTACTCCAGGA
||| | | | || || | || || || | | || | |||||| | |||| | | ||||| ||| |||| | ||||||| |||||||| ||||| |||||||||||||| ||||||||||| |||||||||||||| ||||| ||||||||||||||||| ||||||||||| |
ttatcttgtctcatccttctggataggttctacagtatgttcttctatatggtggtcaagtttcttgaaaaccatgtattttcttattattttcttacagAGTAGCGATGCTGAAGAAGGCAAGTCCAAGAAGGGGCAATATGAAGGACCAGATATGGACTTGGCTGCCATGCTTGAAAGGGATGTCCTGGATTCTACCC-----
upper sequence: GRMZM2G054715_T02 (Zea mays), 3'ss of exon 1
lower sequence: GLYMA08G22210.1 (Glycine max), 3'ss of exon 2
cacttatatttttttgcgggcaaattgccagcta--ctgactggcttctaatgataaagtttttgaaaaatcttccttttccaattcttt---tttctagagtagTGATGCTGAGGAAGGTAAGTCCAAGAAGGGTCAATATGAAGGGCCAGATATGGACTTAGCTGCAATGCTTGAAAGGGATGTTCTGGATTCTACTCCAGGA
| | || |||| | | | || | ||| | | ||| | || | | | | | | || | | ||| | |||||||||| || |||||||| |||||| |||||||||||| || ||| || || |||||||||||||||||||| || | || | |||
ttccctttgcttattgcatcccttattctagattgtttgagaaacatttaacttcatagatatgtggttgtgtccttacaattgctcatggaatggacagAATGGTGATGCTGAAGATGGTAAGTCAAAGAAGCTTCAATATGAAGGTCCTGATCCTGAATTGGCTGCAATGCTTGAAAGGGACGTGTTAGAAACCTCTC-----
upper sequence: GRMZM2G054715_T02 (Zea mays), 3'ss of exon 1
lower sequence: GLYMA07G03820.1 (Glycine max), 3'ss of exon 2
cacttatatttttttgcgggcaaattgccagcta--ctgactggcttctaatgataaagtttttgaaaaatcttccttttccaattcttt---tttctagagtagTGATGCTGAGGAAGGTAAGTCCAAGAAGGGTCAATATGAAGGGCCAGATATGGACTTAGCTGCAATGCTTGAAAGGGATGTTCTGGATTCTACTCCAGGA
| | || |||| | | || || ||| | | ||| || | | | | | | || | | ||| | | |||||||| || |||||||| |||||| |||||||||||| || ||| || || |||||||||||||||||||| || | || | |||
tgccctttgcttattgcatcccttagtctagatagtttgagaaacgtttaacttcttagatatgtggttgtgtccttacaattgctcatggaatggacagAATGGCGATGCTGAAGATGGTAAGTCAAAGAAGCCTCAATATGAAGGTCCTGATCCAGAATTGGCTGCAATGCTTGAAAGGGACGTGTTAGAAACCTCTC-----
upper sequence: GRMZM2G054715_T02 (Zea mays), 3'ss of exon 1
lower sequence: Vv09s0002g05260.t01 (Vitis vinifera), 3'ss of exon 2
cacttatatttttttgcgggcaaattgccagctactgactggcttctaatga--taaagtttttgaaaaatct---tccttttccaattcttt--tttctagagtagTGATGCTGAGGAAGGTAAGTCCAAGAAGGGTCAATATGAAGGGCCAGATATGGACTTAGCTGCAATGCTTGAAAGGGATGTTCTGGATTCTACTCCAGGA
|| | | ||| | | ||| | | || || ||| ||| | |||| | || | ||| |||| | || | | || ||||| | |||||||||| || || || || |||| || || ||||| || || ||| ||||| |||||||||||||||||||||||| |||| ||| |
-accttcactttgt-aagaaataatagtgatgtaacttgtgtgttcatttgaccttcagttagtcaatattctgcttcctaatttgtttgtgtaattgctagAATGGTGATGCTGAAGATGGAAAATCAAAGAGGGCACAGTATGAGGGACCTGATCCAGACTTGGCTGCAATGCTTGAAAGGGATGTTTTGGAGACTAGCC----- atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ctaatgataaagtttttgaaaaatcttccttttccaattcttttttctagagtagTGATGCTGAGGAAGGTAAGTCCAAGAAGGGTCAATATGAAGGGCCAGATATGGACTTAGCTGCAATGCTTGAAAGGGATGTTCTGGATTCTACTCCAGGA
ttctaat putative branch site (score: 2)
tcttccttttccaatt putative PPT
ataaagtttttgaaaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
cacttatatttttttgcgggcaaattgccagctactgactggcttctaatgataaagtttttgaaaaatcttccttttccaattcttttttctagagtagTGATGCTGAGGAAGGTAAGTCCAAGAAGGGTCAATATGAAGGGCCAGATATGGACTTAGCTGCAATGCTTGAAAGGGATGTTCTGGATTCTACTCCAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGC