Sequence
atgc intronic sequence ATGC exonic sequence...caatcaaaatgagcctgaaaaagaatcaaaattagttcttgttttcacattttcctttatgttttgtactgatgaacttaaaactaaatttcatatgcagACTGTTGCACTTGTTGGAGAGAGTGGTAGTGGTAAGTCAACAATAATTTCTTTGCTCGAGAGATTCTACGATCCAGATTCTGGTACAATCTCACTGGATG
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AC233882.1_FGT003 (Zea mays), 3'ss of exon 13
lower sequence: LOC_Os01g50080.1 (Oryza sativa), 3'ss of exon 9
caatcaaaatgagcctgaaaaagaatcaaaattagttcttgttttcacattttcctttatgttt-----tgtactgatgaacttaaaactaaatttcatatgcagACTGTTGCACTTGTTGGAGAGAGTGGTAGTGGTAAGTCAACAATAATTTCTTTGCTCGAGAGATTCTACGATCCAGATTCTGGTACAATCTCACTGGATG
| |||||| | | || ||| ||||| | | ||| |||||||||||| || |||||||| || |||| || | ||||||||||||||||||||||||||||||||| || ||||| ||||| ||| ||||| ||||||| ||| ||||||| || ||| ||||||| ||||||||||| ||
-ctttcaaatgaaaattaccaataatacaaatttctctatattt----attttcctttataattaaacttgtactgacatgctataaaccaattgtcatatgcagACTGTTGCACTTGTTGGAGAGAGCGGCAGTGGAAAGTCCACAGTAATTGCTTTGCTGGAGCGATTCTATGACCCACATTCTGGCACAATCTCACTAGACA
upper sequence: AC233882.1_FGT003 (Zea mays), 3'ss of exon 13
lower sequence: Vv10s0003g02540.t01 (Vitis vinifera), 3'ss of exon 11
------------------------------------------caatcaaaatgagcctgaaaaagaatcaaaattagttcttgttttcacattttcctttatgttttgtactgatgaacttaaaactaaatttcatatgcagACTGTTGCACTTGTTGGAGAGAGTGGTAGTGGTAAGTCAACAATAATTTCTTTGCTCGAGAGATTCTACGATCCAGATTCTGGTACAATCTCACTGGATG
|||| | ||| | | | || ||| | | | | | | | | | | ||| | || | ||||| | | | | | ||||||||||||| || |||||||||||||||||||| ||||| ||| |||| | | ||||| |||||| | || || || ||| || ||||||||
gtatcaccattcttattttggatattttcttagatattttaccaattcacatgc-tcaatataggacctaaacctgatcaatatatgtccttgagcatcagtatttcat-ttgctcaacttca--tgatctgttgtttgcagACTGTTGCCCTAGTTGGAGAGAGTGGTAGTGGGAAGTCGACAGTAATCAGCCTAATAGAGAGGTTCTACAACCCTGAATCGGGTCGTATACTACTGGATG
upper sequence: AC233882.1_FGT003 (Zea mays), 3'ss of exon 13
lower sequence: Vv10s0003g02570.t01 (Vitis vinifera), 3'ss of exon 13
caatcaaaatgagcctgaaaaagaatcaaaattagttcttgttttcacattttcctttatgttttgtactgatgaacttaaaactaaatttcatatgcagACTGTTGCACTTGTTGGAGAGAGTGGTAGTGGTAAGTCAACAATAATTTCTTTGCTCGAGAGATTCTACGATCCAGATTCTGGTACAATCTCACTGGATG
| || || ||| | | | ||| | | || | ||| | | | | | || | | || ||||||||||||| || |||||||||||||||||||| ||||| ||| |||| | || |||||||||||| |||| ||||| ||| || | ||||||||
------gtactcgctattgttcgacccaacttcaataggtgtatgtatatatcattttttttgtctcatttatcagtta----------tttgcctgcagACTGTTGCTCTAGTTGGAGAGAGTGGTAGTGGAAAGTCGACAGTAATCAGCCTACTAGAGAGATTCTACAATCCTGATTCCGGTCATATATTACTGGATG
upper sequence: AC233882.1_FGT003 (Zea mays), 3'ss of exon 13
lower sequence: Vv10s0003g02580.t01 (Vitis vinifera), 3'ss of exon 11
caatcaaaatgagcctgaaaaagaatcaaaattagttcttgttttcacattttcctttatgttttgtactgatgaacttaaaactaaatttcatatgcagACTGTTGCACTTGTTGGAGAGAGTGGTAGTGGTAAGTCAACAATAATTTCTTTGCTCGAGAGATTCTACGATCCAGATTCTGGTACAATCTCACTGGATG
|| | || ||| | | ||| ||| | || ||| | | || || | ||||| ||||||| || |||||||||||||| ||||| ||||||||| | || | | ||||| ||||| |||| ||||| || | || | ||||||
----------------------------------gtaatcacttccac-tgctgcttgtcttttaactttcatttgcttgac-ttgaaaatcttttgcagGCTGTTGCTCTAGTTGGAGAGAGTGGAAGTGGGAAGTCAACAGTGATCAGCCTAATAGAGAGGTTCTATAATCCTGATTCCGGGGCTATATTGTTGGATG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.cacattttcctttatgttttgtactgatgaacttaaaactaaatttcatatgcagACTGTTGCACTTGTTGGAGAGAGTGGTAGTGGTAAGTCAACAATAATTTCTTTGCTCGAGAGATTCTACGATCCAGATTCTGGTACAATCTCACTGGATG
aactaaa putative branch site (score: 2)
aacttaaaactaaatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
caatcaaaatgagcctgaaaaagaatcaaaattagttcttgttttcacattttcctttatgttttgtactgatgaacttaaaactaaatttcatatgcagACTGTTGCACTTGTTGGAGAGAGTGGTAGTGGTAAGTCAACAATAATTTCTTTGCTCGAGAGATTCTACGATCCAGATTCTGGTACAATCTCACTGGATG
-aatcaaa
- - - - - - gcctgaa
- - - - - - - - - - - - - - - - - gttcttg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgttttg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ctgatga
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aaactaa