Sequence
atgc intronic sequence ATGC exonic sequence...ctgctacttgtttctattgtccgtgactacatgcaataaacaaacccttgctggcagccctggtgttcactaactctcttattccattctgtgttcaaagGAATGGGTGACCGACAATTCTTTTATCATATCACCAAGGATCACTTTTGAAGTCAGTGTTCGTCTTCTTGGTGGTTTGATGGCATTGGGATATACTATAG
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GRMZM2G147430_T02 (Zea mays), 3'ss of exon 6
lower sequence: LOC_Os02g47860.2 (Oryza sativa), 3'ss of exon 6
ctgctacttgtttctattgtccgtgactacatgcaataaacaaacccttgctg--gcagccctggtgttca--ctaactctcttattccattctgtgttcaaagGAATGGGTGACCGACAATTCTTTTATCATATCACCAAGGATCACTTTTGAAGTCAGTGTTCGTCTTCTTGGTGGTTTGATGGCATTGGGATATACTATAG
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----agcttagatatatactcctttgctataccttattatcatatcgtatttgcaataattttgaaatttgtgttcactaacttgtgttattgataatttgaagGAGTGGGTGACCGATAATCCTTTTATCATATCACCAAGGATTACGTTTGAAGTCAGTGTTCGTCTTCTTGGAGGTTTGATGGCATTGGGATATACTATAG
upper sequence: GRMZM2G147430_T02 (Zea mays), 3'ss of exon 6
lower sequence: GLYMA05G07610.1 (Glycine max), 3'ss of exon 7
ctgctacttgtttctattgtccgtgactacatgcaataaacaaacccttgctggcag---ccctggtgttcactaactctcttattccattctgtgttcaaagGAATGGGTGACCGACAATTCTTTTATCATATCACCAAGGATCACTTTTGAAGTCAGTGTTCGTCTTCTTGGTGGTTTGATGGCATTGGGATATACTATAG
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ctactcctgccttcttgagtttgaaatt-tgcggaa-aagtttgcagttagaagcaaaattactgaaaaacctctataatgttagtgcatttt-tgttttcagGAATGGGTGACAGATAGTCCATTCATAATATCACCTAGAATTACTTTTGAAGTCAGCGTGCGCCTTCTTGGAGGGCTGATGGCCTTGGGATACACAATTG
upper sequence: GRMZM2G147430_T02 (Zea mays), 3'ss of exon 6
lower sequence: GLYMA02G14110.1 (Glycine max), 3'ss of exon 6
-ctgctacttgtttctattgtccgtgactacatgcaataaacaaacccttgctggcagccctggtgtt-cactaactctcttattccattctgtgttcaaagGAATGGGTGACCGACAATTCTTTTATCATATCACCAAGGATCACTTTTGAAGTCAGTGTTCGTCTTCTTGGTGGTTTGATGGCATTGGGATATACTATAG
|| ||| | | | | | || | | || ||| | | | ||||| | || | || | || ||||||||||||| || || | ||| ||||||||||||| || |||||||| |||||||| || ||||||||||| | ||||| |||||||| || ||||
tttgtgttttgcatattatatatatataccaattccccacacttgat-ttgtggagaatttttacacggtgttaactaattgatgtc-ttataacttttcagGAATGGGTGACAGATAACCCATTTGTCATATCACCAAGAATTACTTTTGAGGTCAGTGTGCGCCTTCTTGGTGGACTAATGGCTTTGGGATACACAATAG
upper sequence: GRMZM2G147430_T02 (Zea mays), 3'ss of exon 6
lower sequence: GLYMA01G09660.1 (Glycine max), 3'ss of exon 6
-----------ctgctacttgtttctattgtccgtg-actacatgcaataaacaaacccttgctggcagccctggtgttcactaactctcttattccattctgtgttcaaagGAATGGGTGACCGACAATTCTTTTATCATATCACCAAGGATCACTTTTGAAGTCAGTGTTCGTCTTCTTGGTGGTTTGATGGCATTGGGATATACTATAG
|| | | | ||| ||| | || | || | || ||| || ||||||| ||||| || | || | || ||||||||||||| || ||| | ||| ||||||||||||| || |||||||| |||||||| || ||||||||||| | ||||| |||||||| || ||||
atatatatatatatatatatataccaattctccatacacgatttgaagagaatgaactttttaca-------tggtgttaactaa-----ttgatgtcttgtaacttttcagGAATGGGTGACAGATAATCCATTTGTCATATCACCAAGAATTACTTTTGAGGTCAGTGTGCGCCTTCTTGGTGGACTAATGGCTTTGGGATACACAATAG
upper sequence: GRMZM2G147430_T02 (Zea mays), 3'ss of exon 6
lower sequence: AT1G26190.1 (Arabidopsis thaliana), 3'ss of exon 6
-------------------------------ctgctacttgtttctattgtccgtgactacatgcaataaacaaacccttgctggcagccctggtgttcactaact--ctcttattccattctgtgttcaaagGAATGGGTGACCGACAATTCTTTTATCATATCACCAAGGATCACTTTTGAAGTCAGTGTTCGTCTTCTTGGTGGTTTGATGGCATTGGGATATACTATAG
|| | | | | || | | | |||| || | | | | || | | | | || | ||| | | |||||||||| || || | | ||||| ||||||| |||||||| || ||||||||||||||||| || |||||||| | |||||||||||||| || ||||
gtttgttcagagtttattttccatgttctcatcaatatgactattcaatatctggaaaagctgacaatccctctgattctggtaagatgcttagtatctggtgaataactgtggttctggttttgacaaccagGAATGGGTTACGGATACTCCTTTTGTCATATCCCCAAGGATTACATTTGAAGTCAGTGTTCGCCTACTTGGTGGGCTCATGGCATTGGGATACACAATAG
upper sequence: GRMZM2G147430_T02 (Zea mays), 3'ss of exon 6
lower sequence: AT1G73980.1 (Arabidopsis thaliana), 3'ss of exon 6
------ctgctacttgtttctattg--tccgtgactacatgcaataaa-caaacccttgctggcagccctggt-gttcactaactctcttatt-ccattct--gtgttcaaagGAATGGGTGACCGACAATTCTTTTATCATATCACCAAGGATCACTTTTGAAGTCAGTGTTCGTCTTCTTGGTGGTTTGATGGCATTGGGATATACTATAG
| ||| ||| | | | || | || | | || | | |||| | | | || | | | | ||| || |||| |||||| |||| ||||| || || | | ||||| |||||||| || || ||||||||||| ||||||||||||||||| || || |||||| |||| ||||| || |
gtttggccaatacctgtccagactagtttttcttctgtaaacaccatatcatatcaaagctgaacgaatggtttattaatttgatgaatgattaccgttctatgtgttcttagGAGTGGGTTACAGATCGTCCATTTATTATATCACCCAGAATAACTTTTGAAGTTAGTGTTCGTCTTCTTGGAGGATTAATGGCACTGGGTTATACCATTG
upper sequence: GRMZM2G147430_T02 (Zea mays), 3'ss of exon 6
lower sequence: Vv01s0010g01080.t01 (Vitis vinifera), 3'ss of exon 5
ctgctacttgtttctatt--gtccgt-gactacatgcaataaaca-aacccttgctggcagccctggtgttcactaactctcttattccattctgtgttcaaagGAATGGGTGACCGACAATTCTTTTATCATATCACCAAGGATCACTTTTGAAGTCAGTGTTCGTCTTCTTGGTGGTTTGATGGCATTGGGATATACTATAG
| ||||| | | | || || ||| | | | | | || || | | | || | || | | | |||| ||| |||||||||| || || ||| | ||| | ||||||||||| || ||||||||||||||||| || ||||||||||| | ||||| ||||| || || ||||
--acaccttgtctttgtctggtttgttaacttcctaaggtcattttagtccatgagaaatacgcgagacttgcccaatctgatcagttggttctcatttc--agGAATGGGTTACTGATAATCCATTTGTTATATCACCAAGAATAACTTTTGAAGTCAGTGTGCGGCTTCTTGGTGGGCTAATGGCCTTGGGGTACACAATAG
upper sequence: GRMZM2G147430_T02 (Zea mays), 3'ss of exon 6
lower sequence: Vv17s0000g04650.t01 (Vitis vinifera), 3'ss of exon 5
ctgctacttgtttctattgtccgtgactacatgcaataaacaaacccttgctggcagccctggtgttcactaactctcttattccattctgt----gttcaaagGAATGGGTGACCGACAATTCTTTTATCATATCACCAAGGATCACTTTTGAAGTCAGTGTTCGTCTTCTTGGTGGTTTGATGGCATTGGGATATACTATAG
| | || | || || | | | | | || || | ||||| | |||| || || |||||| || || |||| ||| |||||||||| || || | | | || ||||| |||||||| || ||||||||||| ||||| || ||||||||||| ||||||| ||||| || || || |
tttgtgttttgctgaataatcttttaaagtagaagaaatgcagacgat-gctgg-ggtgagggtgaa-acgaaatctctt-ctcaatactgtacttgttttcagGAATGGGTTACAGATAGTCCGTTCATCATTTCACCAAGAATAACTTTTGAAGTTAGTGTCCGCCTTCTTGGTGGCCTGATGGCCTTGGGGTACACAATTG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ccttgctggcagccctggtgttcactaactctcttattccattctgtgttcaaagGAATGGGTGACCGACAATTCTTTTATCATATCACCAAGGATCACTTTTGAAGTCAGTGTTCGTCTTCTTGGTGGTTTGATGGCATTGGGATATACTATAG
cactaac putative branch site (score: 1)
tcttatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ctgctacttgtttctattgtccgtgactacatgcaataaacaaacccttgctggcagccctggtgttcactaactctcttattccattctgtgttcaaagGAATGGGTGACCGACAATTCTTTTATCATATCACCAAGGATCACTTTTGAAGTCAGTGTTCGTCTTCTTGGTGGTTTGATGGCATTGGGATATACTATAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG