Sequence
atgc intronic sequence ATGC exonic sequence...gccagttttcattttcctctcctggcacccccacccaacattatgtgcttatgtagttctttcttcccttacatttttttgtattccatgacactgctagAAATCACGGATGGGGATGCCAAATCTGGAGGCAACCTTTGAAACACTGGTTGATGCATTTGTGTTCCTGGACAAGAATAAGGATGGTTATGTGAGCAAGA
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: Vv19s0015g01200.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GRMZM2G006790_T02 (Zea mays), 3'ss of exon 3
gccagttttcattttcctctcctggcacccccacccaacattatgtgcttatgtagttctttcttcccttacatttttttgtattccatgacactgctagAAATCACGGATGGGGATGCCAAATCTGGAGGCAACCTTTGAAACACTGGTTGATGCATTTGTGTTCCTGGACAAGAATAAGGATGGTTATGTGAGCAAGA
| || | | | | | | | | | | | | | || | | | | | | | | | |||| | |||||| | |||||| ||||||||||| || || |||||||||| ||||| ||| |||| |||||||| ||||| ||||||||||||
agtggagtttgaatatgggtatggagatcggtaagctgctggagatagtcttatgccatttctgttaggagcgtccatgtttcctttacatacttcacagAAGATAAAGATGGGACTAGGAAATCTTGAGGCAACCTTCGAGACCTTGGTTGATGCGTTTGTCTTCTTGGATAAGAATAAAGATGGGTATGTGAGCAAGG
upper sequence: Vv19s0015g01200.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GRMZM2G092929_T01 (Zea mays), 3'ss of exon 1
-gccagttttcattttcctctcctggcacccccacccaacattatgtgcttatgtagttctttcttcccttacatttttttgtattccatgacactgctagAAATCACGGATGGGGATGCCAAATCTGGAGGCAACCTTTGAAACACTGGTTGATGCATTTGTGTTCCTGGACAAGAATAAGGATGGTTATGTGAGCAAGA-
| | ||| | | | |||| | ||| | || | | | | || | || | | | | | | ||| | |||||| | |||||| |||||||| ||||| || |||||||||||||||| ||| |||| | |||||| ||||| ||||||||||||
agatgtactgtgattttttttttttgcactcaggttatgttttagat-ctcttatgccacatctgtcaggagcgttcctgtttcctttacagacttcacagATGATAAAGATGGGACTAGAAAATCTTGAGGCAACTTTTGAGACCTTGGTTGATGCATTTGTCTTCTTGGATA-GAATAAAGATGGGTATGTGAGCAAGGA
upper sequence: Vv19s0015g01200.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA08G33830.2 (Glycine max), 3'ss of exon 3
---gccagttttcattttcctc-tcctggcacccccaccca-acattatgtgcttatgtagttctttcttcccttacatttttttgtattccatgacactgctagAAATCACGGATGGGGATGCCAAATCTGGAGGCAACCTTTGAAACACTGGTTGATGCATTTGTGTTCCTGGACAAGAATAAGGATGGTTATGTGAGCAAGA
| ||| | | |||| || | || ||| | | | | | || || | || | | | | |||||||| ||||||| |||||||||||| || ||||||||||| ||||||| || ||||| || |||||||| ||||||| ||| | |||||||| |||||||| ||||| ||||| |
cagggcagcctagaatttcatcatgcttgcattgataacaataaaccttgaatttccatgttttgctacatcttcaaattttttt-----ccatgacttccctagAAATCACGAATTGGGATGCCAAAGCTGGAGGGCACATTTGAGACTTTGGTTGATACATTTGTATTCTTAGACAAGAACAAGGATGGATATGTCAGCAAAA
upper sequence: Vv19s0015g01200.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA16G16060.1 (Glycine max), 3'ss of exon 4
gccagttttcattttcctctcctggcacccccacccaacattatgtgcttatgtagttctttcttcccttacattttt---ttgtattccatgacactgctagAAATCACGGATGGGGATGCCAAATCTGGAGGCAACCTTTGAAACACTGGTTGATGCATTTGTGTTCCTGGACAAGAATAAGGATGGTTATGTGAGCAAGA
||| | | | | | || | | || | | || | ||| | || ||||| || |||| ||||||||| |||||||||||| || ||||||||||| |||||| || ||||| || |||||||| ||||||| ||||| |||||||| |||||||| ||||| ||||| |
--cagggaagcctagaattttgtcatgcttcctttgataacaataaacct-tgaatttccatgttttgctacatcttcaaattgttttccatgacttccctagAAATCACGAATTGGGATGCCAAAGCTGGAGCGCACATTTGAGACTTTGGTTGATACATTTGTATTCCTAGACAAGAACAAGGATGGATATGTCAGCAAAA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tgcttatgtagttctttcttcccttacatttttttgtattccatgacactgctagAAATCACGGATGGGGATGCCAAATCTGGAGGCAACCTTTGAAACACTGGTTGATGCATTTGTGTTCCTGGACAAGAATAAGGATGGTTATGTGAGCAAGA
ttccatgac putative branch site
ttacatttttttgtat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gccagttttcattttcctctcctggcacccccacccaacattatgtgcttatgtagttctttcttcccttacatttttttgtattccatgacactgctagAAATCACGGATGGGGATGCCAAATCTGGAGGCAACCTTTGAAACACTGGTTGATGCATTTGTGTTCCTGGACAAGAATAAGGATGGTTATGTGAGCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA
- - - - - - - - ctctcct
- - - - - - - - - - - - - - -cccaccc
- - - - - - - - - - - - - - - - - - - - -tatgtgc