Sequence
atgc intronic sequence ATGC exonic sequencegtcactgaacctaaaaaaagtatcgtgtttgttccgcctaacttttggcattatagttctgaaatatttttcattcagtgttcgctgcattctacattagttttcctttcattgttaaggcaagagaatactcatctcttataaccaatgtatcttttgtaaactagGCTTGCAAAAAGCTTGGGAAAATTGAGCTGTCGGATTGTGAAATTTATGCATCTTGTGAGCCATGCCCAATGTGTTTTGGTGCTGTTCATCTATCCCGGA
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GRMZM5G840909_T01 (Zea mays), 3'ss of exon 5
lower sequence: LOC_Os03g61810.1 (Oryza sativa), 3'ss of exon 3
gtcactgaacctaaaaaaagtatcgtgtttgttccgcctaacttttggcattatagttctgaaatatttttcattcagtgttcgctgcattctacattagttttcctttcattgttaaggcaagagaatactcatctcttataaccaatgtatcttttgtaaactagGCTTGCAAAAAGCTTGGGAAAATTGAGCTGTCGGATTGTGAAATTTATGCATCTTGTGAGCCATGCCCAATGTGTTTTGGTGCTGTTCATCTATCCCGGA
|||| | || | |||||| |||||||||| | || ||||||| | | || | || |||| ||||| | || ||| |||||||||||||||||||| ||||||||| |||| || |||||||| |||||||| ||||| || |||||||||||||| || ||||| |||||||| ||||
-------------------------------------------------------attctttgccagccaat-ttgggccgataatgcatttaacattagttt-ctttccattgtttggtta---------tcttttcacataataaatgt-ttttctgtgctatagGCTTGCAAAAAGCTTGGAAAAATTGAGTTGTCAGACTGTGAAATGTATGCATCATGTGAACCTTGCCCAATGTGTTTCGGCGCTGTGCATCTATCACGGA
upper sequence: GRMZM5G840909_T01 (Zea mays), 3'ss of exon 5
lower sequence: GLYMA13G17790.1 (Glycine max), 3'ss of exon 3
gtcactgaacctaaaaaaagtatcgtgtttgttccgcctaacttttggcattatagttctgaaatatttttcattcagtgttcgctgcattct-acattagttttcctttcattgttaaggcaagagaatactcatctcttataaccaatgtatcttttgtaaactagGCTTGCAAAAAGCTTGGGAAAATTGAGCTGTCGGATTGTGAAATTTATGCATCTTGTGAGCCATGCCCAATGTGTTTTGGTGCTGTTCATCTATCCCGGA
| | | ||| |||| |||| | | || | | | ||| | | || | ||| | | | |||| || ||| | || || |||||||||| |||||| | | || || || | ||||||||||| ||||| |||||||| || ||||| ||||| |||||||| | || || || || |
-----------------------------------------------------aaatctcgctgtatgactcat---gtgtgcattatttttttatagatgttataaactttatgcagtgtcaaaaaatgattcatg---------cagtgttttcatttta---cagGCTTGCAAGAAGCTTAAGCAGATAGAACTTGCTGATTGTGAAATATATGCTTCTTGTGAACCTTGCCCCATGTGCTTTGGTGCAATCCACCTTTCTCGAA
upper sequence: GRMZM5G840909_T01 (Zea mays), 3'ss of exon 5
lower sequence: GLYMA17G04720.2 (Glycine max), 3'ss of exon 3
gtcactgaacctaaaaaaagtatcgtgtttgttccgcctaacttttggcattatagttctgaaatatttttcattcagtgttcgctgcattctacat-tagttttcctttcattgt-taaggcaagagaatactcatctcttataaccaatgtatcttttgtaaactagGCTTGCAAAAAGCTTGGGAAAATTGAGCTGTCGGATTGTGAAATTTATGCATCTTGTGAGCCATGCCCAATGTGTTTTGGTGCTGTTCATCTATCCCGGA
|| || | | | | | | || || ||||| || || | | || || | | || | | | |||| || ||| ||| | | ||||||| || |||||| | | || || || | ||||||||||| ||||| |||||||| || ||||| ||||| |||||||| | || || || || |
------------------------------------------------------agctc---attgtatgactctgtatgccttcttttttctagatataataaactttatgcagtgttaaataaaaaatgattcatg---------cagtgt---tttcatttaacagGCTTGTAAGAAGCTTAAGCAGATAGAACTTGCAGATTGTGAAATATATGCTTCTTGTGAACCTTGCCCCATGTGCTTTGGTGCAATCCACCTTTCTCGAA
upper sequence: GRMZM5G840909_T01 (Zea mays), 3'ss of exon 5
lower sequence: Vv14s0030g01610.t01 (Vitis vinifera), 3'ss of exon 3
gtcactgaacctaaaaaaagtatcgtgtttgttccgcctaacttttggcattatagttctgaaatatttttcattcagtgttcgctgcattctacattagttttcctttcattgttaaggcaagagaatactcatctcttataacc--aatgtatcttttgtaaactagGCTTGCAAAAAGCTTGGGAAAATTGAGCTGTCGGATTGTGAAATTTATGCATCTTGTGAGCCATGCCCAATGTGTTTTGGTGCTGTTCATCTATCCCGGA
|| || || ||| || | || || || | || ||| || | | | | | | | | ||| || |||| | | || | |||| || || ||||| |||||||||| || || |||||||| ||||| ||||||||||| ||||||||||| ||||||||| | ||||| || | |
-------------------------------------------------------------aactagattgtgctcattgaatgacaaat-ctgcaagtgattcacttctcttttcagtg----atactctttgtttctcatgcttggaatgaaaccttcctg---cagGCATGTAAGAAGCTCAATCAAATTGAGCTATCAGACTGTGAAATCTATGCCTCTTGTGAGCCTTGCCCAATGTGCTTTGGTGCTATACATCTTTCAAGAA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tgttaaggcaagagaatactcatctcttataaccaatgtatcttttgtaaactagGCTTGCAAAAAGCTTGGGAAAATTGAGCTGTCGGATTGTGAAATTTATGCATCTTGTGAGCCATGCCCAATGTGTTTTGGTGCTGTTCATCTATCCCGGA
ttataac putative branch site (score: 2)
tatctttt putative PPT
ttttgtaaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtcactgaacctaaaaaaagtatcgtgtttgttccgcctaacttttggcattatagttctgaaatatttttcattcagtgttcgctgcattctacattagttttcctttcattgttaaggcaagagaatactcatctcttataaccaatgtatcttttgtaaactagGCTTGCAAAAAGCTTGGGAAAATTGAGCTGTCGGATTGTGAAATTTATGCATCTTGTGAGCCATGCCCAATGTGTTTTGGTGCTGTTCATCTATCCCGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT