Sequence
atgc intronic sequence ATGC exonic sequence...agatccatttgcttgatattataaattttctttctttgctgcaagcttgaccaacctggccaagacttattgttttcctgtcacatgttttccttttcagTTCTTTATCGTGTTGTCGTGCATAATTGCTGTCGGGACCAACCTAAGCCAGTTCATATGCATCGGAAGATTCACGGCCGTCTCGTTCCAAGTCCTAGGTC
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GRMZM2G089630_T01 (Zea mays), 3'ss of exon 6
lower sequence: LOC_Os05g12490.1 (Oryza sativa), 3'ss of exon 5
----agatccatttgcttgatattataaattttctttctttgctgcaagcttgaccaacctggccaagacttattgttttcctgtcacatgt-tttccttttcagTTCTTTATCGTGTTGTCGTGCATAATTGCTGTCGGGACCAACCTAAGCCAGTTCATATGCATCGGAAGATTCACGGCCGTCTCGTTCCAAGTCCTAGGTC
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tggaggatatattt--tttataatctgttgttgccatgaccattactatttttatcg---tggcagggcctaacattttctttttttcatctacctgcattgtagTTCTTCATCATACTGTCGTGCATAATTGCTGTTGGGACCAACCTTAGCCAATTCATATGCATCGGAAGATTTACAGCAGTCTCGTTCCAAGTTCTAGGCC
upper sequence: GRMZM2G089630_T01 (Zea mays), 3'ss of exon 6
lower sequence: LOC_Os02g40090.4 (Oryza sativa), 3'ss of exon 5
agatccatttgcttgatattataaattttcttt-ctttgctgcaagcttgac-caacctggccaagacttattgttttcctgtcacatgttttccttttcagTTCTTTATCGTGTTGTCGTGCATAATTGCTGTCGGGACCAACCTAAGCCAGTTCATATGCATCGGAAGATTCACGGCCGTCTCGTTCCAAGTCCTAGGTC
||| | | | | || ||| |||| | | | || | | | |||| || ||| |||| || ||| |||||||| || || |||||||||| ||||||||| |||||||| |||||||||||||||||||| ||||||||||| || ||||| || ||||| ||||| |
-tatcatagcagtgcagacctgatgttcccttgacttttacatattccttacatgagcaaactgggactaatgctttcttcttcactcacttaa-tttccagTTCTTCATTGTATTGTCGTGCACAATTGCTGTTGGGACCAATCTAAGCCAGTTCATATGCATTGGAAGATTCACAGCTGTCTCATTTCAAGTTCTAGGCC
upper sequence: GRMZM2G089630_T01 (Zea mays), 3'ss of exon 6
lower sequence: GLYMA05G31940.1 (Glycine max), 3'ss of exon 6
agatccatttgcttgatattataaattttcttt-ctttgctgcaagcttgac--caacctggccaagacttattgttttcctgtcacatgttttcctttt-cagTTCTTTATCGTGTTGTCGTGCATAATTGCTGTCGGGACCAACCTAAGCCAGTTCATATGCATCGGAAGATTCACGGCCGTCTCGTTCCAAGTCCTAGGTC
| ||||| || ||| | |||| | | | | | || | | ||| | | | | || || | ||| ||| ||||| || ||| | | || |||| || || || ||||| ||||| ||||||||||| ||||| || || |||||||| || || ||||||||||| || |
gaaatcattttct----attttgaattccatatgcataggcctttgcctaatgttaactttacaatagtactatattgaactaatctgcttcttctgtttgcagTTGTTCATCATTATCTCTTGCACCATCGCAGTAGGGACAAACCTCAGCCAGTTCATCTGCATTGGCAGGTTCACGGCTGTATCTTTCCAAGTCCTTGGAC
upper sequence: GRMZM2G089630_T01 (Zea mays), 3'ss of exon 6
lower sequence: GLYMA06G15280.2 (Glycine max), 3'ss of exon 5
agatccatttgcttgatattataaattttctttctttgctgcaagcttgaccaacctggcc----aagacttattgttttcctgtcacatgttttcctttt-cagTTCTTTATCGTGTTGTCGTGCATAATTGCTGTCGGGACCAACCTAAGCCAGTTCATATGCATCGGAAGATTCACGGCCGTCTCGTTCCAAGTCCTAGGTC
|| ||| | | || || ||| ||| | || | | |||| || ||| | | | | ||||| || ||| | |||| |||| || || || ||||| ||||| ||||||||||| ||||| || || |||||||| || ||||||||||||| ||||
-----tataaatactgtatagtttacctttactcaagaaaacaataatgaatactgtgactcctggaatactattattaaactgagctgctcctgctgtctgcagTTGTTCATCATTCTGTCTTGCACTATCGCAGTAGGGACAAACCTCAGCCAGTTCATCTGCATTGGTAGGTTCACGGCTGTAACGTTCCAAGTCCTTGGTC
upper sequence: GRMZM2G089630_T01 (Zea mays), 3'ss of exon 6
lower sequence: AT4G09810.1 (Arabidopsis thaliana), 3'ss of exon 5
agatccatttgcttgatattataaattttctttctttgctgca--agcttgaccaacctggccaa-gacttattgttt---tcctgtcacatgtt--ttccttttcagTTCTTTATCGTGTTGTCGTGCATAATTGCTGTCGGGACCAACCTAAGCCAGTTCATATGCATCGGAAGATTCACGGCCGTCTCGTTCCAAGTCCTAGGTC
| | ||| |||| | ||| || || | | ||| || | | || || || || ||| | | | || || | | | | ||| | ||||| | ||||||| ||| || ||||||| ||||| ||||||||||| |||||||| |||||||| || || || ||||||||||| || |
------agaagggtga--ttatcaccttttttctgttatcaaatgggtttgcacatcgactctaatgaattgttctttgtattcaataacttggtgatgattctgcagATGTTTATAACCCTCTCGTGCACAATAGCAATCGGGACAAACCTGAGCCAGTTCATCTGCATCGGGAGATTCACAGCAGTGTCATTCCAAGTCCTGGGCC
upper sequence: GRMZM2G089630_T01 (Zea mays), 3'ss of exon 6
lower sequence: AT1G34020.1 (Arabidopsis thaliana), 3'ss of exon 5
agatccatttgcttgatattataaattttctttctttgctgcaagcttgaccaacctggccaagacttattg-----ttttcctgtcacatgttttc---cttttcagTTCTTTATCGTGTTGTCGTGCATAATTGCTGTCGGGACCAACCTAAGCCAGTTCATATGCATCGGAAGATTCACGGCCGTCTCGTTCCAAGTCCTAGGTC
|| || | ||| ||| | | ||| |||| | || ||| ||| || | | | | ||| | |||| | | ||| | ||||| ||||||||| ||| || | || |||||||||||||||||||| ||||||||||||||||| || || ||||||||||| || || |
-------cttagttaac-ttacaaaccatttctctgtgcttaaggccaaaccgtgctgtacatacatggtagaaacttattcgaacctaatgtccctgaattctgcagCTGTTTATAACCCTGTCGTGCACAATAGCGATTGGAACCAACCTAAGCCAGTTCATCTGCATCGGAAGATTCACAGCTGTATCGTTCCAAGTGCTGGGAC
upper sequence: GRMZM2G089630_T01 (Zea mays), 3'ss of exon 6
lower sequence: Vv18s0072g00080.t01 (Vitis vinifera), 3'ss of exon 4
agatccatttgcttgatattataaattttctttctttgctgcaagcttgaccaacctggccaagacttattgttttcctgtcacat-gtttt--ccttttcagTTCTTTATCGTGTTGTCGTGCATAATTGCTGTCGGGACCAACCTAAGCCAGTTCATATGCATCGGAAGATTCACGGCCGTCTCGTTCCAAGTCCTAGGTC
| | |||| || | | | || || | ||| | ||| | || ||||| | || | | || | | | || || | ||| ||| | ||||| | | || || | || || || ||||||||||| ||||||||||||||||| || |||||||| || ||||| || ||||| || || |
-ggtgaatttcctctagttcactttattcctagcattgtgccttgct--atttgtctttacaagaatgatctctcacttgcctcgttgtcttggcttttgcagATATTTATAATCCTTTCATGTACTATCGCGGTAGGGACCAACCTCAGCCAGTTCATATGCATTGGTAGATTCACAGCTGTCTCCTTTCAAGTACTTGGCC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.cttgaccaacctggccaagacttattgttttcctgtcacatgttttccttttcagTTCTTTATCGTGTTGTCGTGCATAATTGCTGTCGGGACCAACCTAAGCCAGTTCATATGCATCGGAAGATTCACGGCCGTCTCGTTCCAAGTCCTAGGTC
gcttgac putative branch site (score: 4)
catgttttccttttc putative PPT
ttattgtttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
agatccatttgcttgatattataaattttctttctttgctgcaagcttgaccaacctggccaagacttattgttttcctgtcacatgttttccttttcagTTCTTTATCGTGTTGTCGTGCATAATTGCTGTCGGGACCAACCTAAGCCAGTTCATATGCATCGGAAGATTCACGGCCGTCTCGTTCCAAGTCCTAGGTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA
- - - - -tgcttga
- - - - - - - - - - - - - - - - - -ttgctgc
- - - - - - - - - - - - - - - - - - - - - - - - - ccaacct
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -catgttt