Sequence
atgc intronic sequence ATGC exonic sequencegtaattcagtgacagctggatattctactcaactgtattttcgaagtcatgcaaattggcattatttttttaatcttcttgtagGTAGGCAAAAACCTTCATGTTCTAAGCCAGATTGAGGGTGTTGACCTTGATATGTACAAAGAAACTGTTCTTCCAAGGATATTAGAGCAG
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GRMZM5G825524_T02 (Zea mays), 3'ss of exon 6
lower sequence: LOC_Os03g58700.1 (Oryza sativa), 3'ss of exon 6
gtaat--tcagtgacagctggatattctactcaactgtattttcgaagtcatgcaaat--tggcattatttttttaatcttcttgtagGTAGGCAAAAACCTTCATGTTCTAAGCCAGATTGAGGGTGTTGACCTTGATATGTACAAAGAAACTGTTCTTCCAAGGATATTAGAGCAG
||||| ||| | ||| || || |||| | || | || | ||||| ||| || | || | || || |||||||||||||||||||| |||||||||||||||||||||||||||||||| ||||||||||||||||| ||||||||||||||||| |||
gtaatcatcaattaca--tgtattccctacactacatgttctttggtgtcatttcaatgacattgctactgttctttcttttttctagGTAGGCAAAAACCTTCACGTTCTAAGCCAGATTGAGGGTGTTGACCTTGACATGTACAAAGAAACTGTCCTTCCAAGGATATTAGAACAG
upper sequence: GRMZM5G825524_T02 (Zea mays), 3'ss of exon 6
lower sequence: GLYMA17G37870.1 (Glycine max), 3'ss of exon 7
gtaattcagtgaca--gctggatattctactcaa-ctgtattttcgaagtcatg-caaattggcattatttttttaatcttc-----ttgtagGTAGGCAAAAACCTTCATGTTCTAAGCCAGATTGAGGGTGTTGACCTTGATATGTACAAAGAAACTGTTCTTCCAAGGATATTAGAGCAG
||||| | | | || | || | || | | | || | | || | || | | | ||| | | | |||||||| ||||| || |||||||| || ||||| ||||| || |||||||| ||||||||||| || || ||||| || | |||||||||
gtaatataaaaatatgatactatctcctgatgaagcaatgtgttacacattttgatagataagttatgtgatttccttttctgaaattattagGTAGGGAAAAATCTACATGTTCTGAGTCAGATAGAGGGCGTGGACCTTGAGATGTACAAAGACACCGTCCTTCCTAGTGTCTTAGAGCAG
upper sequence: GRMZM5G825524_T02 (Zea mays), 3'ss of exon 6
lower sequence: GLYMA11G08390.1 (Glycine max), 3'ss of exon 6
---------gtaattcagtgacagctggatattctactc---aactgtattttcgaagtcatgcaaattggca-------ttatttttttaatcttcttg------tagGTAGGCAAAAACCTTCATGTTCTAAGCCAGATTGAGGGTGTTGACCTTGATATGTACAAAGAAACTGTTCTTCCAAGGATATTAGAGCAG
| | | | | | | | ||| | ||||| || | |||| || | || |||||| ||| | ||||| ||||| || ||||||||||| || ||||| |||||||||||||| |||||||||||||| ||| ||||| || || | ||||||
gtaatacctgaagcttgttactggtttgcttctctgcaatggggttgtataaatgatgaaatgcttatagaaggcttttcttgcttttttgtccttgatacataattagGTTGGCAAGAATCTTCATGTTCTCAGTCAGATAGAGGGTGTTGACCTAGATATGTACAAAGATGTTGTGCTTCCCAGAGTACTGGAGCAG
upper sequence: GRMZM5G825524_T02 (Zea mays), 3'ss of exon 6
lower sequence: GLYMA01G36870.1 (Glycine max), 3'ss of exon 6
-------------------------gtaattcagtgacagctggatattctactcaactgtattttcgaagtcatgcaaattggcattatt-tttttaatcttcttgtagGTAGGCAAAAACCTTCATGTTCTAAGCCAGATTGAGGGTGTTGACCTTGATATGTACAAAGAAACTGTTCTTCCAAGGATATTAGAGCAG
| ||| || || || | | || | || | || | || || || | || || | ||||| || || || ||||||||||| || ||||| |||||||||||||| |||||||||||||| |||| ||||| || || | ||||||
gtaatacctgaagcctagaactggtttgcttctctg-caatggggttgtttaaatgatgaaatgcttatagaaggcttctcttgcttttttgtccttgatacattattagGTTGGAAAGAATCTTCATGTTCTCAGTCAGATAGAGGGTGTTGACCTAGATATGTACAAAGATGCTGTGCTTCCCAGAGTACTGGAGCAG
upper sequence: GRMZM5G825524_T02 (Zea mays), 3'ss of exon 6
lower sequence: AT1G75850.1 (Arabidopsis thaliana), 3'ss of exon 6
gtaattcagtgacagctggatattctactcaactgtattttcgaagtcatgcaaattggcattatttttttaatcttcttgtagGTAGGCAAAAACCTTCATGTTCTAAGCCAGATTGAGGGTGTTGACCTTGATATGTACAAAGAAACTGTTCTTCCAAGGATATTAGAGCAG
|||| | || || | || | || | ||| | | || ||| | | | ||| | | | || |||| || ||||| || ||||||||| | ||||| || |||||||||||||| ||||||||||| ||||||||||| ||| | |||||||||
gtaacatcgataccactacttgaattagtatcctatttttgctatgtactgcccactaagttgtatttaatgttttcctctcagGTTGGAAAAAATCTGCATGTTCTAGGACAGATAGAAGGTGTTGACCTTGAGATGTACAAAGAGACTGTTCTTCCTAGGGTCTTAGAGCAG
upper sequence: GRMZM5G825524_T02 (Zea mays), 3'ss of exon 6
lower sequence: Vv04s0023g03870.t01 (Vitis vinifera), 3'ss of exon 6
gtaat-tcagtgac----agctggatattctactc------aactgtat-----tttcgaagtcatgcaaattggcattatttttt---taatcttcttgt-agGTAGGCAAAAACCTTCATGTTCTAAGCCAGATTGAGGGTGTTGACCTTGATATGTACAAAGAAACTGTTCTTCCAAGGATATTAGAGCAG
||||| || | || | || | || |||| |||||| | || | | | || | | |||| | ||||| | | |||| || || ||||| ||||| || ||||| | ||||||||||| || ||||||||||||||||| || ||||| || | || ||||||
gtaataccaataacctgaaactagttacgtcactccaatagaactgtgtgcatattctgtgcacttataaccgactactcttttgccgctgatcttttcattagGTTGGGAAGAACCTGCATGTCCTTGGCCAGCTAGAGGGTGTTGATCTCGATATGTACAAAGAAACAGTCCTTCCCAGAGTTTTGGAGCAG
upper sequence: GRMZM5G825524_T02 (Zea mays), 3'ss of exon 6
lower sequence: Vv18s0001g14680.t01 (Vitis vinifera), 3'ss of exon 6
gtaattcagtgacagctggatattctactcaactgtattttcgaagtcatgcaaattggcattat-------ttttttaatcttcttgtagGTAGGCAAAAACCTTCATGTTCTAAGCCAGATTGAGGGTGTTGACCTTGATATGTACAAAGAAACTGTTCTTCCAAGGATATTAGAGCAG
|||| | |||| | | | | || || | | | | |||| | | || | | |||||||| || || || || |||||||| || |||||||||||| |||||||||| ||||| ||||| ||||||||||| ||| | |||||||||
gtaagatcagataatctgggtctatgtaataccactagttggagcagtgtctatagagaagttatggtgctgtcctgtattttctttgtagGTTGGGAAGAATCTACATGTTCTCAGTCAGATTGAGGGTATTGACCTTGAAATGTATAAAGATACTGTTCTTCCCAGGGTCTTAGAGCAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.caactgtattttcgaagtcatgcaaattggcattatttttttaatcttcttgtagGTAGGCAAAAACCTTCATGTTCTAAGCCAGATTGAGGGTGTTGACCTTGATATGTACAAAGAAACTGTTCTTCCAAGGATATTAGAGCAG
ttttaat putative branch site (score: 3)
tttttttaatcttctt CT-rich tract
attatttttttaatct 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaattcagtgacagctggatattctactcaactgtattttcgaagtcatgcaaattggcattatttttttaatcttcttgtagGTAGGCAAAAACCTTCATGTTCTAAGCCAGATTGAGGGTGTTGACCTTGATATGTACAAAGAAACTGTTCTTCCAAGGATATTAGAGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCAG