Sequence
atgc intronic sequence ATGC exonic sequence...caacactttactgattatatatcatcaatgatgtctcattgtcatttgcatagtggtgttttatgctgttacagtttttaacttgcttgtactgtgttagGAATGGATAATGGAACAGTGGGAGAGAAATTTCTATATCACTGCACTGGCTGGTGCGAATAATGGAAGCTCTTTGGTGATTATGTCAAGAG
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GRMZM2G045259_T02 (Zea mays), 3'ss of exon 12
lower sequence: LOC_Os01g10150.1 (Oryza sativa), 3'ss of exon 12
caacactttactgattatatatcatcaatgatgtctcattgtcatttgcatagtggtgtttta----tgctgttacagtttttaacttgcttgtactgtgttagGAATGGATAATGGAACAGTGGGAGAGAAATTTCTATATCACTGCACTGGCTGGTGCGAATAATGGAAGCTCTTTGGTGATTATGTCAAGAG
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catctaatgcctaatcgcggcggctaaccggcgcctggagctgacttttagaacactgagataaatgtataatcacaacttt-aactg---tgcgctttgatagGAATGGATAATGGAGCAGTGGGAGAGAAATTACTATATTACTTCTTTGGCTGGTTCAAATAATGGAAGCTCGGTGGTGATCATGTCAACAG
upper sequence: GRMZM2G045259_T02 (Zea mays), 3'ss of exon 12
lower sequence: Vv09s0002g03680.t01 (Vitis vinifera), 3'ss of exon 12
-----------------------------------------------------------------------caacactttactgattatatatcatcaatgatgtctcattg---tcatttgcata-gtggtgttttatgctgttacagtttttaacttgcttgtactgtgt-tagGAATGGATAATGGAACAGTGGGAGAGAAATTTCTATATCACTGCACTGGCTGGTGCGAATAATGGAAGCTCTTTGGTGATTATGTCAAGAG
|| || | | | |||| | ||| | | || || | | | ||| | ||||| || | || || |||| |||| | |||||||||||||||||||||||||||| ||| |||||||||| |||| | || || || | |||||| ||||| | || | ||||| | |
gtgcgtctcatttcttttgtttaacccatggcatacatatttatctttacatgtgtcatgcaattaaatttcatcagtatgatcgaggcatatta-caaggctacttctttcagcttactgttatacatttaattttaacaagtgatcaattaatctttttttgttctgtctatagGAATGGATAATGGAACAGTGGGAGAAAAACTTCTATATCAGTGCAATAGCAGGAGCTACTAATGGGAGCTCACTAGTTGTAATGTCTAAGG
upper sequence: GRMZM2G045259_T02 (Zea mays), 3'ss of exon 12
lower sequence: PP1S66_174V6.1 (Physcomitrella patens), 3'ss of exon 12
-caacactttactgattatatatcatcaatgatgtctcattgtcatttgcatagtggtgttttatgctgttacagtttttaacttgcttgt-actgtgtta--gGAATGGATAATGGAACAGTGGGAGAGAAATTTCTATATCACTGCACTGGCTGGTGCGAATAATGGAAGCTCTTTGGTGATTATGTCAAGAG
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gtaagtgctcagtgattgtttagtgtttctgcttgttgtttttgaaggatctagttg-gccctcttcttttgtggaaattaacatggtcattggtattctacagGAGTGGATCATGGAACAGTGGGAAAAGAATTTCTATATCAGTGCAATTGCTGGAGCTAATAATGGGAGCTCTTTGGTCGTCATGTCGAAAG
upper sequence: GRMZM2G045259_T02 (Zea mays), 3'ss of exon 12
lower sequence: PP1S131_16V6.1 (Physcomitrella patens), 3'ss of exon 12
---------caacactttactga--ttatatatcatcaatgatgtctcattgtcatttgcatagtggtgttttatgctgt----tacagtttttaacttgcttgtactgtgttagGAATGGATAATGGAACAGTGGGAGAGAAATTTCTATATCACTGCACTGGCTGGTGCGAATAATGGAAGCTCTTTGGTGATTATGTCAAGAG
| || | || | | | ||| | | ||| | | | | | || | | | | | | | || | | |||| ||||| |||||||||||||| | ||||||||||||| ||| | |||||||| ||||| |||||||| ||||| | ||||| | ||
gtgggtgtgtggtgtctcgctcaagttttgggtagtatatgcagcttgtcgttcaatgatagaacagctatccctgttatgcgccatgccctcacattgagtcatatttttacagGAGTGGATCATGGAACAGTGGGAAAAGAATTTCTATATCAGTGCCATCGCTGGTGCAAATAACGGAAGCTCCTTGGTCGTCATGTCTAAAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttgcatagtggtgttttatgctgttacagtttttaacttgcttgtactgtgttagGAATGGATAATGGAACAGTGGGAGAGAAATTTCTATATCACTGCACTGGCTGGTGCGAATAATGGAAGCTCTTTGGTGATTATGTCAAGAG
ttttaac putative branch site (score: 2)
tttttaactt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
caacactttactgattatatatcatcaatgatgtctcattgtcatttgcatagtggtgttttatgctgttacagtttttaacttgcttgtactgtgttagGAATGGATAATGGAACAGTGGGAGAGAAATTTCTATATCACTGCACTGGCTGGTGCGAATAATGGAAGCTCTTTGGTGATTATGTCAAGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG