Sequence
atgc intronic sequence ATGC exonic sequence...ggggcattattaatttattatgcatcagggaacacattctatttttttcactgatactataaaagttttaatttcttatttgcttttaatcctagtgcagGAGTTGATCCTCCATCATCTCGTGATCCTCCTGTGCTGCTTGCAGCACCAGCATCAAATGTTCTATCATTGCAGAACTCAGCACTGTTGGACTCATCCCT
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GRMZM2G052078_T02 (Zea mays), 3'ss of exon 13
lower sequence: LOC_Os04g42840.1 (Oryza sativa), 3'ss of exon 13
------------------------------------------------ggggcattatta---atttattatgcatcagggaaca-cattct-atttttttcactgatactataaaagttttaatttcttatttgcttttaatcctagtgcagGAGTTGATCCTCCATCATCTCGTGATCCTCCTGTGCTGCTTGCAGCACCAGCATCAAATGTTCTATCATTGCAGAACTCAGCACTGTTGGACTCATCCCT
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gtattcttttaactgcttagttgtcaattactgttaagtaatagaaatggccttttatcatgtatttcctggtcattgactgacaatattatcatcttagttttctatgataaaaaaaatc-agtttcttatttccttttaatcctagtgcagGGGTTGATCCTCCATCGTCTCGTGATCCTCCTGTTCCGCTTGCAGCAACAGCTTCAAATCATCTGTCCTTACAGAATTCAGCACTGCTCGACTCATCTGT
upper sequence: GRMZM2G052078_T02 (Zea mays), 3'ss of exon 13
lower sequence: GLYMA19G35460.1 (Glycine max), 3'ss of exon 13
------------------------ggggcattattaatttattatgcatcagg----gaacacattctatt-----tttttcactgatactataaaagttttaatttctta---tttgcttttaat---cctagtgcagGAGTTGATCCTCCATCATCTCGTGATCCTCCTGTGCTGCTTGCAGCACCAGCATCAAATGTTCTATCA-------TTGCAGAACTCAGCACTGTTGGACTCATCCCT
||||| | | | ||||| || ||||| || | | | | || | | |||| ||| | ||| ||| || ||| | ||||||||||||||||| |||||||||||||||||||| ||| | | ||| | || ||||| ||| ||| || | ||||| | ||| ||| |
gtaccacataagttttcctgttagttatttttatttgtacctcaattttcaggactagatgtcattcaatggttgatctgttagtgtttttttaaactatttgagcggttaaatttttctcttattgcccctagtgcagGAGTTGACCCTCCATCATCTCGTGATCCACCTTTCCCTGCTGCTGTCCCCGCATCTAATCATCTGACAAGCTCTTTAACAGAATCAACTACTTCTGGCAT-------
upper sequence: GRMZM2G052078_T02 (Zea mays), 3'ss of exon 13
lower sequence: GLYMA13G19230.1 (Glycine max), 3'ss of exon 13
----------------------------------------------------ggggcattattaatttattatgcatcagggaacacattctatttttttcactgatactataaaagttttaatttcttatttgcttttaatcctagtgcagGAGTTGATCCTCCATCATCTCGTGATCC----TCCTGTGCTGCT--TGCAGCACC--AGCATCAAAT--GTTCTATCATTGCAGAACTCAGCACTGTTGGACTCATCCCT
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gtaccaaataagtttacttgttaaatatatatattttttctaccacattgttctggacttgttgccattcaacaattgatgaagctagtgatatggttttta--aactttgtgagcggctaaat---ttatctcttattgcccctagtgcagGAGTTGACCCTCCCTCATCTCGTGATCCACCATTCCCTGCTGCTGTCACAGCATCTAATCATCTGACTAGCTCTTTAACGGCAGAATCAACTGCAGCTGG----------
upper sequence: GRMZM2G052078_T02 (Zea mays), 3'ss of exon 13
lower sequence: GLYMA03G32710.1 (Glycine max), 3'ss of exon 13
------------------------------------------ggggcattattaatttattatgcatcagggaacacattctatttttttcactgatactataaaagttttaatttcttatttgcttttaatcctagtgcagGAGTTGATCCTCCATCATCTCGTGATCCTCCTGTGCTGCTTGCAGCACCAGCATCAAATGTTCTATCATTGCAGAACTCAGCACTGTTGGACTCATCCCT
| | | || || | || | | || | |||| | | | | | | | ||||| | || || ||||||||||||||||| |||||||||||||||||||| ||| | | || | || ||||| ||| ||| || || || | | |||
gtacaacataagttttcctgttatatatttttatttttacctcaattttcaggacttgatgccattcaatggttgatctgttagtgttttttcaaactatttgagcggctaaatttttctctta---ttgcccctagtgcagGAGTTGACCCTCCATCATCTCGTGATCCACCTTTCCCTGCAGCTGTCCCCGCATCTAATCATCTGACAAGCTCTTTAACAACAGAATCAACTACTTCCGG
upper sequence: GRMZM2G052078_T02 (Zea mays), 3'ss of exon 13
lower sequence: GLYMA10G04850.1 (Glycine max), 3'ss of exon 13
----------------------------------------------------ggggcattattaatttattatgcatcagggaacacattctatttttttcactgatactataaaagttttaatttcttatttgcttttaatcctagtgcagGAGTTGATCCTCCATCATCTCGTGATCCTCCTGTGCTGCTTGCAGCACCAGCATCAAATGTTCTATCATTGCAGAACTCAGCACTGTTGGACTCATCCCT
|| || || | | | | | | | ||| |||| | | | | | | | ||| |||| | | || ||||||||||||||||| ||||| |||||||||||||| || | | ||| | ||||||| ||| |||| | | || | ||||
gtaccaaataagtttacttgttaaatatatatattttttctacctcattgttctggacttgttgccattcaacaattgatgatgctagtgatatggttttta--aactttgtgagcggctaaat---ttatctcttattgcccctagtgcagGAGTTGACCCTCCCTCATCTCGTGATCCACCATTCCCTGCTGCTGTCACAGCATCTAATCATCTAACTAGCTCTTTAACGACAGAATCAACTGCATCTGG
upper sequence: GRMZM2G052078_T02 (Zea mays), 3'ss of exon 13
lower sequence: AT2G20190.1 (Arabidopsis thaliana), 3'ss of exon 13
ggggcattattaatttattatgcatcagggaacacattctattttt------ttcactgatactataaaagttttaatttc---------ttatttgcttttaatcctagtgcagGAGTTGATCCTCCATCATCTCGTGATCCTCCTGTGCTGCTTGCAGCACCAGCATCAAATGTTCTATCATTGCAGAACTCAGCACTGTTGGACTCATCCCT-----
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------gtattgagtttctttccttatgaaagtacagtttgtttttgaaacgtcctttaacatgagctaagatatccttgcgcagctaaattgtcttctttttcccctagtgcagGAGTTGACCCTCCATCGTCTCGTGATCCTCCTTTCCATGCTGTTGCTCCAGCATCCAATAGTCACACA---AGTAGCGCAGC--TGCTGAATCAACACATAGTAT
upper sequence: GRMZM2G052078_T02 (Zea mays), 3'ss of exon 13
lower sequence: Vv07s0005g05030.t01 (Vitis vinifera), 3'ss of exon 10
----------------------------------------------------------------------------------------ggggcattattaatttattatgcatcagggaacac-attctatttttttcactgatac----tataaaagttttaatttcttatttgcttttaatcctagtgcagGAGTTGATCCTCCATCATCTCGTGATCCTCCTGTGCTGCTTGCAGCACCAGCATCAAAT-GTTCTATCATTGCAGAACTCAGCACTGTTGGACTCATCCCT
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gtattgaatggttttgtcaattagattattatctttgatcataatattaatttgactgtcaatctatgaagctattcaatggtttactgttgaatcactatctgattgaccaatggtcaaaacgaagctgtctttaatgtttgaacaatttatgaacggctaagtttttctctta---ttgcccctagcgcagGAGTTGACCCTCCATCATCTCGTGATCCTCCATTTCCTCTTGCTGTTCCAGCATCAAATCAACTTACAAACACTTCGAT-GGTAGAATCAAATGCTTCTAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tttcactgatactataaaagttttaatttcttatttgcttttaatcctagtgcagGAGTTGATCCTCCATCATCTCGTGATCCTCCTGTGCTGCTTGCAGCACCAGCATCAAATGTTCTATCATTGCAGAACTCAGCACTGTTGGACTCATCCCT
ttttaat putative branch site (score: 3)
atactataaaagtttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ggggcattattaatttattatgcatcagggaacacattctatttttttcactgatactataaaagttttaatttcttatttgcttttaatcctagtgcagGAGTTGATCCTCCATCATCTCGTGATCCTCCTGTGCTGCTTGCAGCACCAGCATCAAATGTTCTATCATTGCAGAACTCAGCACTGTTGGACTCATCCCT
- - - - - - - - - - -gcatcag
- - - - - - - - - - - - - - - - cacattc
- - - - - - - - - - - - - - - - - - - - - - - ttcactg