Sequence
atgc intronic sequence ATGC exonic sequence...ctaggtgaatagttctaacctattcccagaattgtgaacatgctaccagttgaaaatgccttccgtgaaagcaatgtttgcaccatgtattgtgtaacagAGTAAGGATGCCGAGGTGATGCTGAAGATGGGAAGCACAACTGACAAGCGTGAACAGTATAGATTGATGAGAGATGCTATGGAGAAAAG
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GRMZM5G806649_T02 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os01g16510.1 (Oryza sativa), 3'ss of exon 2
------ctaggtgaatagttctaacctattc-ccagaattgtgaacatgctaccagttgaaaatgccttccgtgaaagcaatgtttgcaccatgtattgtgtaacagAGTAAGGATGCCGAGGTGATGCTGAAGATGGGAAGCACAACTGACAAGCGTGAACAGTATAGATTGATGAGAGATGCTATGGAGAAAAG-----------
||||||| | || || ||| || || ||| | ||| | | ||||| || |||| || | | || | || | | | | || |||||| || || || || |||||| |||||||||| ||||| || ||||||||||| ||||||||||||||||||||||| |||||||||||
ctattttgaggtgaacatttatatccttttttcctgaactccttacaccaaataaaatgaaa-tgtcttcagttacaacattatt-gtgctgtatttt-----acagAGCAAAGACGCTGAAGTGATGTTGAAGATGGGGAGCACCACAGACAAGCGTGAGCAGTATAGATTGATGAGAGATGCAATGGAGAAAAGATTCATCCGGG
upper sequence: GRMZM5G806649_T02 (Zea mays), 3'ss of exon 2
lower sequence: GLYMA17G09580.1 (Glycine max), 3'ss of exon 2
ctaggtgaatagttctaacctattcccagaattgtgaacatgctaccagttgaaaatgccttccgtgaaagcaatgtttgcaccatgtat----tgtgtaac-agAGTAAGGATGCCGAGGTGATGCTGAAGATGGGAAGCACAACTGACAAGCGTGAACAGTATAGATTGATGAGAGATGCTATGGAGAAAAG-----------
||||| | || | | | | ||||| ||||| | | || | | | | | | | || | | | | ||||| | |||| |||||||| || || ||| |||| | || |||||| ||||||||||| || ||| |||||||||||||||| ||||||||| |
-taggt--tttttttcatgccaaccatgttattgtaaacat--tgcttgtctagattatcccaattaattgtggtgatcttaaggaatttcacatgtgttgctagAGCAAGGATGCAGAAGTTATGTTGAAACTTGGGAGCACAGAAGACAAGCGTGAGCAATATCGATTGATGAGAGATGCAATGGAGAAACGATTCATTCGAG
upper sequence: GRMZM5G806649_T02 (Zea mays), 3'ss of exon 2
lower sequence: GLYMA05G02350.1 (Glycine max), 3'ss of exon 2
ctaggtgaatagttctaacctattcccagaattgtgaacatgctaccagttgaaaatgccttccgtgaaagcaatgtttgcaccatgtattgtg-----taacagAGTAAGGATGCCGAGGTGATGCTGAAGATGGGAAGCACAACTGACAAGCGTGAACAGTATAGATTGATGAGAGATGCTATGGAGAAAAG-----------
||||| | | | | | | ||||| ||||| | | || | | | | | | | || | | | | || |||| |||||||| || || ||| |||| | || ||||| ||||| ||||| || ||| |||||||||||||||| ||||||||| |
-taggttctttttcttg--ccaaccatgttattgtaaacat--tgcttgtctagattatcccatttaattgtggtgatcttaaggaatttcacacatgttactagAGCAAGGATGCAGAAGTTATGTTGAAACTTGGGAGCACTGAAGACAAACGTGAGCAATATCGATTGATGAGAGATGCAATGGAGAAACGATTCATTCGAG
upper sequence: GRMZM5G806649_T02 (Zea mays), 3'ss of exon 2
lower sequence: AT5G63000.1 (Arabidopsis thaliana), 3'ss of exon 2
--------------------------------------------------------------------------------ctaggtgaat---agttctaacctattcccagaat-tgtgaacat-----gctaccagttgaaaatgccttccgtgaaagcaatgtttgcaccatgtattgtgtaacagAGTAAGGATGCCGAGGTGATGCTGAAGATGGGAAGCACAACTGACAAGCGTGAACAGTATAGATTGATGAGAGATGCTATGGAGAAAAG-----------
|| |||| | || ||| || | || || | | || | || || |||| || |||| ||| || ||| | || ||||||| || ||||| || |||||| |||||||||| || ||| || ||||||||||| | || |||||| ||||||| |||||||||||
gtatgtctgctttcaatttcagattcaagctcgttacttgtccttgagatttgtgtttcgattccactaccttggtgtaacttagtgacttctggtactagactgaactcataagatatcaaagtttaagacttttagctgaatattatttcctgtgttaaaatcagtgtgt-gtgtggtttgaaacagAGCAAAGATGCAGAAGTGATGTTGAAGATGGGTAGTACACAGGATAAGCGTGAACAACACAGGTTGATGCGAGATGCAATGGAGAAAAGGTTCATCCGAG
upper sequence: GRMZM5G806649_T02 (Zea mays), 3'ss of exon 2
lower sequence: Vv17s0000g08630.t01 (Vitis vinifera), 3'ss of exon 2
----ctaggtgaatagttctaacctattcccagaattgtgaacatgctaccagttgaaaatgccttccg--tgaaagcaatgtttgcaccatgtattgtgtaacagAGTAAGGATGCCGAGGTGATGCTGAAGATGGGAAGCACAACTGACAAGCGTGAACAGTATAGATTGATGAGAGATGCTATGGAGAAAAG-----------
||||| | ||| | | | | | || | || | ||| | | | | ||| || || |||| | | ||||| |||||||| || |||||||||||| | || |||||| | |||||||| || || ||||| || ||||||||||| |||||||||||
gattttaggtcttagtaaacagtgtatcttaaataattttcattgtcttcttgtgcacaatccaattaaacttttaatgatgattaca--atgt----tatggcagAGCAAGGATGCAGAAGTGATGCTGAAGCTTGGGAGCACACCAGACAAGCGGGAGCAATATAGGTTAATGAGAGATGCAATGGAGAAAAGGTTCATCCGAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ccagttgaaaatgccttccgtgaaagcaatgtttgcaccatgtattgtgtaacagAGTAAGGATGCCGAGGTGATGCTGAAGATGGGAAGCACAACTGACAAGCGTGAACAGTATAGATTGATGAGAGATGCTATGGAGAAAAG
tgaaaat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ctaggtgaatagttctaacctattcccagaattgtgaacatgctaccagttgaaaatgccttccgtgaaagcaatgtttgcaccatgtattgtgtaacagAGTAAGGATGCCGAGGTGATGCTGAAGATGGGAAGCACAACTGACAAGCGTGAACAGTATAGATTGATGAGAGATGCTATGGAGAAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA