Sequence
atgc intronic sequence ATGC exonic sequence...tcatagataataaaatcaggtcggttcactttaaaggtgccacgctcggcaatgtggagaaccatacattgttaaatgatctttttttgtctattttcagGTGTGATAGCAATTGTTGTGGCAAATCCAACTGATCTTGTTAAAGTTAGGTTGCAAGCTGATGGAAAGGCTAACACTGTCAAGAGGAGTTATTCTGGAGC
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GRMZM2G165629_T02 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os01g74640.3 (Oryza sativa), 3'ss of exon 3
---------------------------------------------------------------------------------tcatagataataaaatcaggtcgg---ttcac-tttaaaggtgccacgctcg--gcaatgtggagaacca--tacattgttaaatga--tctttttttgtctattttcagGTGTGATAGCAATTGTTGTGGCAAATCCAACTGATCTTGTTAAAGTTAGGTTGCAAGCTGATGGAAAGGCTAACACTGTCAAGAGGAGTTATTCTGGAGC
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gtgggtacttttccctatccgtttctctttgctgcactttctcaataatttgtcacatattaaattgcttttgctaattaaatgcagccaaccagtttacatccaaatttcatgtgttaaggacttaaggtaggtgcactatgcacaagtaaatatactcttatattaattaccgttctatatattcatagGTGTCATAGCAATTGTTGTGGCAAATCCAACTGATCTTGTCAAAGTGAGATTGCAAGCTGATGGAAAGGCCACCACTGTCAAGAGGCACTATTCTGGAGC
upper sequence: GRMZM2G165629_T02 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA18G42220.1 (Glycine max), 3'ss of exon 2
-------------------------------------------------------------------------------------tcatagataataaaatcag--gtcggttcactttaaaggtgccacgctcggcaatgtggagaaccatacattgttaaatgatctttttttgt-ctattttcagGTGTGATAGCAATTGTTGTGGCAAATCCAACTGATCTTGTTAAAGTTAGGTTGCAAGCTGATGGAAAGGCTAACACTGTCAAG---AGGAGTTATTCTGGAGC
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ggtaaaggccaattctggacattgtaggaattttttttctatacactaatatgtgaatttgtttccggatctgtggagtgtcaacttcttgctagcaggagcatatgttatttctgtctagaattccgattcattatgcaaaagcaaaac-tataacattaagccacttgaacttgtgttatcaacaGGTGCTATGGCAATTGCAGTGGCGAATCCAACTGATCTTGTGAAAGTTAGACTTCAAGCAGAAGGAAAATTACCTCCTGGTGTGCCCAGGCGTTACTCTG----
upper sequence: GRMZM2G165629_T02 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA07G17380.1 (Glycine max), 3'ss of exon 2
------------------------------------------------------------------------------------------tcatagataataaaatcaggtcggttcactttaaaggtgccacgctcggcaatgtggagaaccatacattg--ttaaatgatctttttttgtctattttcagGTGTGATAGCAATTGTTGTGGCAAATCCAACTGATCTTGTTAAAGTTAGGTTGCAAGCTGATGGAAAGGCTAACACTGTCAAG---AGGAGTTATTCTGGAGC
| | | || | || | | | ||| | | | || | || | ||| | ||||| | ||| ||| | || || | |||||| || ||||||| ||||||||||||||||||||||| |||||||| | ||||| || ||||| ||| | | | | | || |||||
gtaaagcccaattctggacattgtattgtagtgatggttttttctatatgccaatatgtgaatttgtttcctaatgtgcggagtgtgaacttcttgctagctggagcatacgttatttttgtcaagaattcttgat--acattatgcaaaactctgcattgagccacttgaacttgtgttatcaa----cagGTGCTATGGCAATTGCAGTGGCAAATCCAACTGATCTTGTGAAAGTTAGACTTCAAGCAGAAGGAAAATTGCCTCCTGGCGTGCCCAAGCGCTACTCTGG---
upper sequence: GRMZM2G165629_T02 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA03G14780.1 (Glycine max), 3'ss of exon 3
------------------------------------------------------------tcatagataat--aaaatcaggtcggttcactttaaaggtgccacgctcgg---caatgtggagaaccat-acattg--ttaa--atgatctttttttgtctatttt-----cagGTGTGATAGCAATTGTTGTGGCAAATCCAACTGATCTTGTTAAAGTTAGGTTGCAAGCTGATGGAAAGG---CTAACACTGTCAAGAGGAGTTATTCTGGAGC
|| | |||| | | || ||| || | | | || | | | ||| || | | || | || || || | | | || |||||| | ||||||| |||||||||||||| |||||||| |||||||| | |||||||| ||||| || ||| ||| | || |||||
gtaaatctcaatgctggaaattgtgggaataatttgtatatgtgtgctattatatgagtttcttttctaatctatggattatttactttttcttaggggcatcttgtgttattcctatctaaatactcatcgcaataactcaatcacgaactcgttcaatttgtcttgtcaacagGTGCTTTTGCAATTGCAGTGGCAAATCCAACCGATCTTGTCAAAGTTAGACTTCAAGCTGAAGGAAAATTACCTCCTGGTGTTCCCAGGCGCTACTCTGG---
upper sequence: GRMZM2G165629_T02 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA01G27120.1 (Glycine max), 3'ss of exon 2
-----------------------------------------------------------------------tcatagataataaaatcaggtc--ggttcactttaaag-gtgccacgctcggcaatgtggagaaccatacattgttaaatgatctttttttgtct-attttcagGTGTGATAGCAATTGTTGTGGCAAATCCAACTGATCTTGTTAAAGTTAGGTTGCAAGCTGATGGAAAGG---CTAACACTGTCAAGAGGAGTTATTCTGGAGC
|| ||| || | | || | || | | || || | | || | || | |||| ||||||| | |||||| | ||||||| ||||||||||||||||||||||| |||||||| | ||||| || ||||| || ||| ||| | || |||||
gtaaatctcaatgctggaaactgtgggaatattttgtatatatattctattctatgagtttcttttctcatctatggattatttactttttcttaggaggatcttgtattattcccatctaaatactcattgcaataactcaatcataaactcctcgaatttgtcttgtcaacagGTGCTTTTGCAATTGCAGTGGCAAATCCAACTGATCTTGTCAAAGTTAGACTTCAAGCAGAAGGAAAATTACCTCCTGGTGTTCCCAGGCGGTACTCTGG---
upper sequence: GRMZM2G165629_T02 (Zea mays), 3'ss of exon 3
lower sequence: AT5G58970.2 (Arabidopsis thaliana), 3'ss of exon 3
tcatagataataaaatcaggtcggttcactttaaaggtgccacgctcggcaatgtggagaaccat--acattgttaaatga--tctttttttgtctatttt----cagGTGTGATAGCAATTGTTGTGGCAAATCCAACTGATCTTGTTAAAGTTAGGTTGCAAGCTGATGGAAAGGCTAACACTG---TCAAGAGGAGTTATTCTGGAGC
| | |||| || || | ||| | || | | | | | | ||| || | ||| | || || | |||| |||| | | |||| | ||||| ||| |||| || |||||||||||||||||||||||| || | ||| | || |||||| ||| | ||| ||||| | ||
---------gtgagctcagttc--ttaattttgatagtctcttggaagtaacttgagtgaatgattgagattataaagggaattattttattgtgtgtgacacaacagGAGCTATAGCTATTATTGTAGCTAATCCAACTGATCTTGTTAAAGTTCGGCTTCAATCAGAAGGAAAGTTACCGGCTGGGGTTCCTAGGCGTTATGCAGG---
upper sequence: GRMZM2G165629_T02 (Zea mays), 3'ss of exon 3
lower sequence: Vv06s0004g05940.t01 (Vitis vinifera), 3'ss of exon 3
-----------------------------------------------------tcatagataataaaatcaggtcggttcactttaaaggt--------gccacgctcggcaatgtggagaaccatacattgttaaatgatctttttttgtctattttcagGTGTGATAGCAATTGTTGTGGCAAATCCAACTGATCTTGTTAAAGTTAGGTTGCAAGCTGATGGAAAG--GCTAAC-ACTGTCAAGAGGAGTTATTCTGGAGC
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gtcagttacatttggttaccatccttttggttgatgcatgatgaatttagataacaactgtactagcatactgtttttcccatataaagagtcaaataaactatctccagtgattctttgcttcaaaataagttaaattggtgtttctttccta---acagGAGCAATAGCAATTGCAGTCGCAAATCCTACTGATCTTGTAAAAGTTCGGCTTCAAGCTGAAGGAAAATTGCCACCTGGGGTTCCAAGGCGTTACACTGG--- atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tcggcaatgtggagaaccatacattgttaaatgatctttttttgtctattttcagGTGTGATAGCAATTGTTGTGGCAAATCCAACTGATCTTGTTAAAGTTAGGTTGCAAGCTGATGGAAAGGCTAACACTGTCAAGAGGAGTTATTCTGGAGC
tctttttttgtctatt CT-rich tract
attgttaaatgatctt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tcatagataataaaatcaggtcggttcactttaaaggtgccacgctcggcaatgtggagaaccatacattgttaaatgatctttttttgtctattttcagGTGTGATAGCAATTGTTGTGGCAAATCCAACTGATCTTGTTAAAGTTAGGTTGCAAGCTGATGGAAAGGCTAACACTGTCAAGAGGAGTTATTCTGGAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG