Sequence
atgc intronic sequence ATGC exonic sequencegtgagtgacacatctctacatatttgtcttgtcttctcatggcattatattaaatatgcagtatttgcagcacctattattatctttgtttctagtggttaggaagatgattattcattgtgcctgtgtctgcggtttgcacctctgtcctattctaaagcaatgtctctacaaatgcagGAAATCCAAGAGTGACACCAGAGGTTACCAGGGATGTCTGCTTGCTTGCCAGAATGATGGCATCAAACTTGTACTGCTCTCAGATTGAGGATCTCATGTT
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GRMZM2G473001_T02 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os09g14670.1 (Oryza sativa), 3'ss of exon 4
gtgagtgacacatctctacatatttgtcttgtcttctcatggcattatattaaatatgcagtatttgcagcacctattattatctttgtttctagtggttaggaagatgattattcattgtgcctgtgtctgcggtttgcacctctgtcctattctaaagcaatgtctctacaaatgcagGAAATCCAAGAGTGACACCAGAGGTTACCAGGGATGTCTGCTTGCTTGCCAGAATGATGGCATCAAACTTGTACTGCTCTCAGATTGAGGATCTCATGTT
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gtgagaaacatatctat-----tttgt--tgttggttcttagcactatgccttata---aataattacagcacaatgaatcctctttagatgttgtctttaaattactaccacttaggagataccatgtctgta---tgcac-----tctaaatttcaaatgaccttt--------acagGAAATCCAAGAGTCACACCAGAGGTTACAAGGGATGTCTGCTTGCTTGCAAGAATGATGGCAGCAAACTTGTATTGCTCACAAATTGAGGATCTCATGTT
upper sequence: GRMZM2G473001_T02 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA13G36670.1 (Glycine max), 3'ss of exon 5
----------------------gtgagtgacacatctctacatatttgtcttgtcttctcatggcattatattaaatatgcag-tatttgca-gcacctattattatctttgtttctagtggttaggaagatgattattcattgtgcctgtgtctgcggtttgcacctctgtcctattctaaagcaatgtct--ctacaaatgcagGAAATCCAAGAGTGACACCAGAGGTTACCAGGGATGTCTGCTTGCTTGCCAGAATGATGGCATCAAACTTGTACTGCTCTCAGATTGAGGATCTCATGTT
| | || ||| | ||| | || | | || | ||| || || |||| | || | ||| | || | ||| || ||| | | |||| || || | | | | || ||| | ||||||| | | || ||| ||||| ||||| || || || |||||||||||||| || ||||| || ||||||||||| | || |||||| ||||||||| || |||||||||||
gtatctttcttttggctaagaaattaaagaaacaagcttttttatctaactctttgtgacaattccttactttttgcccccaaatattcatatagactaaatatctttttcagcttcagt--tttggacaccgcctcagagatgtggct-----tgtaatatacttattagtttctatcttacaaaatgtctaatttgcattgtagGTAATCCTAGAGTAACCCCTGAAGTTACCAGGGATGTGTGTTTGCTGGCTAGAATGATGGCTGCTAATGTGTACTTCTCTCAGATAGAAGATCTCATGTT
upper sequence: GRMZM2G473001_T02 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA06G33380.1 (Glycine max), 3'ss of exon 4
gtgagtgacacatctctacatatttgtcttgtcttctcatggcattatattaaatatgcagtatttgcagcacctattattatctttgtttctagtggttaggaagatgattattcattgtgcctgtgtctgcggtttgcacctctgtcctattctaaagcaatgtctctacaaatgcagGAAATCCAAGAGTGACACCAGAGGTTACCAGGGATGTCTGCTTGCTTGCCAGAATGATGGCATCAAACTTGTACTGCTCTCAGATTGAGGATCTCATGTT
|| || || |||| | ||| || | | | | ||| | | | | | | |||| | | | |||| | ||||||| ||||||||||| || ||||| || || || ||||| ||||| | || ||||||||||| | |||||||||| ||| ||||| ||| |||| |||||
------------------------------------------------------------------------actgctacctaggttatttcagttacttattaaaaggtgtcatgattctattaagcttctccgaaagtgtgtgtgtctaactatgtt-caatat-------gatgcagGCAATCCAAGAGTAACTCCAGAAGTGACAAGAGATGTTTGCTTATTGGCTAGAATGATGGCTGCTAACTTGTACTACTCCCAGATAGAGAATCTTATGTT
upper sequence: GRMZM2G473001_T02 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA20G09810.1 (Glycine max), 3'ss of exon 5
gtgagtgacacatctctacatatttgtcttgtcttctcatggcattatattaaatatgcagtatttgcagcacctattattatctttgtttctagtggttaggaagatgattattcattgtgcctgtgtctgcggtttgcacctctgtcctattctaaagcaatgtctctacaaatgcagGAAATCCAAGAGTGACACCAGAGGTTACCAGGGATGTCTGCTTGCTTGCCAGAATGATGGCATCAAACTTGTACTGCTCTCAGATTGAGGATCTCATGTT
|| || | ||||| | ||| || | | | | ||| || | ||| | | || | | | | |||| | ||||||| ||||||||||| || || || || ||||| ||||| ||||| | || ||||||||||| | |||||||||| ||| ||||| |||||||| |||||
------------------------------------------------------------------------actgctagctaggtagtttcagttatttactaaaaggtatcatgattctgttatgcttctcggaaagtgtgtgtgcctaactatgtt-caatat-------gatgcagGCAATCCAAGAGTAACTCCTGAAGTGACCAGAGATGTTTGCTTATTGGCTAGAATGATGGCTGCTAACTTGTACTACTCCCAGATAGAGGATCTTATGTT
upper sequence: GRMZM2G473001_T02 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA06G43050.1 (Glycine max), 3'ss of exon 4
gtgagtgacacatctctacatatttgtcttgtcttctcatggcattatattaaatatgcagtatttgc-agcacctattattatctttgtttctagtggttaggaagatgattattcattgtgcctgtgtctgcggtttgcacctctgtcctattctaaagcaatgtctctacaaatgcagGAAATCCAAGAGTGACACCAGAGGTTACCAGGGATGTCTGCTTGCTTGCCAGAATGATGGCATCAAACTTGTACTGCTCTCAGATTGAGGATCTCATGTT
| ||| | | | ||| | ||| |||| | || || || || || | | | | | |||||| ||||| ||||| | | |||||| || || || || || ||||| ||||| |||||||| || ||||| || ||||||||||| | || ||||||| ||||||||||||||||||||||||
---------------------------------------------------------------tgtgccaaaatcccttaaacataatccttcaagtgct----gaggtgttttctcgttcc-----taacagtgaatca-acctct-cactattt--gtctaatgtgtgt-----tgcagGTAACCCCAGGGTAACTCCAGAAGTTACAAGGGATGTGTGTTTGCTGGCTAGAATGATGGCTGCTAATTTGTACTTCTCTCAGATTGAGGATCTCATGTT
upper sequence: GRMZM2G473001_T02 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA12G33820.1 (Glycine max), 3'ss of exon 4
----------------------gtgagtgacacatctctacatatttgtcttgtcttctcatggcattatattaaatatgcagtatttgcagcacctattattatctttgtttctagtggttaggaagatgattattcattgtgcctgtgtctgcggtttgcacctctgtcctattctaaagcaatgtct--ctacaaatgcagGAAATCCAAGAGTGACACCAGAGGTTACCAGGGATGTCTGCTTGCTTGCCAGAATGATGGCATCAAACTTGTACTGCTCTCAGATTGAGGATCTCATGTT
| | ||| ||| | |||| || | | || | ||| || | || || | || | ||| || | || | ||| || ||| || | |||| || || | | | | || ||| | ||||||| | | || ||| ||||| ||||| || || || ||||| |||||||| || ||||| || ||||||||||| | || |||||| ||||||||| ||||||||||||||
gtatctttcttttccctaagaaattaatgaaacaagcatttttattaacctctttgttacaattccttactttttgtccccaa-atgttca-tatgtat-atctttttcaacttcagt--ttgggacactgcctcagagatgtggct-----tgtaatatacttattggtttctatcttacaaaatgtctaatttgcattgtagGTAATCCTAGAGTAACCCCTGAAGTTACAAGGGATGTGTGTTTGCTGGCTAGAATGATGGCTGCTAATATGTACTTCTCTCAGATAGAGGATCTCATGTT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gtgtctgcggtttgcacctctgtcctattctaaagcaatgtctctacaaatgcagGAAATCCAAGAGTGACACCAGAGGTTACCAGGGATGTCTGCTTGCTTGCCAGAATGATGGCATCAAACTTGTACTGCTCTCAGATTGAGGATCTCATGTT
ttctaaa putative branch site (score: 2)
tctctac putative PPT
tattctaaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtgagtgacacatctctacatatttgtcttgtcttctcatggcattatattaaatatgcagtatttgcagcacctattattatctttgtttctagtggttaggaagatgattattcattgtgcctgtgtctgcggtttgcacctctgtcctattctaaagcaatgtctctacaaatgcagGAAATCCAAGAGTGACACCAGAGGTTACCAGGGATGTCTGCTTGCTTGCCAGAATGATGGCATCAAACTTGTACTGCTCTCAGATTGAGGATCTCATGTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAT