Sequence
atgc intronic sequence ATGC exonic sequence...gtaatgctcaagaacacaccaggatgattggcatggaagatatcattttgaccttttttctcttactatttttttatataaactaacttcttttctgcagAGCATGCGCAGGATGTCACAGAGAGATTGGTCACGGGCGTTTTCTCAGTTGCATGGGAGCTGTTTGGCATCCGGAATGTTTTCGTTGCCATGCATGTAGT
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GRMZM2G017845_T04 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os06g08400.1 (Oryza sativa), 3'ss of exon 4
-----gtaatgctcaagaaca-caccaggatgattggcatggaagatatcattttgaccttttttctcttactatttttttatataaactaacttcttttctgcagAGCATGCGCAGGATGTCACAGAGAGATTGGTCACGGGCGTTTTCTCAGTTGCATGGGAGCTGTTTGGCATCCGGAATGTTTTCGTTGCCATGCATGTAGT
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ctgcactgatacttggggatggtaattggtaagcgagaatgggatgctgcgagttg---cttttactcttactgtttcttaatatatac--gcttatttcct-cagGACTTGTGCCGGATGTCACAGTGAGATTGGTCATGGGCGTTTCCTTAGTTGCATGGGAGCTGTTTGGCATCCAGAATGTTTTCGCTGTCATGCTTGTAAT
upper sequence: GRMZM2G017845_T04 (Zea mays), 3'ss of exon 4
lower sequence: GLYMA12G19010.1 (Glycine max), 3'ss of exon 3
gtaatgctcaagaacacaccaggatgattggcatggaagatatcattttgaccttttttctcttactatttttttatataaactaactt----cttttctgcagAGCATGCGCAGGATGTCACAGAGAGATTGGTCACGGGCGTTTTCTCAGTTGCATGGGAGCTGTTTGGCATCCGGAATGTTTTCGTTGCCATGCATGTAGT
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-tcaagatagaagacat-ctataatgttttcttttcataaattc--ttgaattttacttataaaaacagaggttaaacctggttcttgcaaaatgttcttgcagAATCTGTGCTGGCTGTAATGCTGAGATTAGCCATGGAAGATTTTTGAGTTGCATGGGAGGTTATTGGCATCCGGAATGCTTTTGTTGCCATGCTTGCAAA
upper sequence: GRMZM2G017845_T04 (Zea mays), 3'ss of exon 4
lower sequence: GLYMA16G25750.1 (Glycine max), 3'ss of exon 4
gtaatgctcaagaacacaccaggatgattggcatggaagatatcattttgaccttttttctcttactatttttttatataaact----aacttcttttctgcagAGCATGCGCAGGATGTCACAGAGAGATTGGTCACGGGCGTTTTCTCAGTTGCATGGGAGCTGTTTGGCATCCGGAATGTTTTCGTTGCCATGCATGTAGT
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atcaagat--agaagacatttataatgtttccttttcataaat--tcttgaattttacttataaaacagaggctaaaactggttcttgggaaatgtgcttgcagAATCTGTGCTGGCTGCAATTCCGAGATTGGCCATGGAAGATTTTTGAGTTGCATGGGAGGTTATTGGCATCCAGAATGTTTTTGTTGCCATGCTTGCAAA
upper sequence: GRMZM2G017845_T04 (Zea mays), 3'ss of exon 4
lower sequence: AT4G36860.1 (Arabidopsis thaliana), 3'ss of exon 4
---------------------------gtaatgctcaaga----acacaccaggatgattggcatggaagatatcattttgaccttttttctcttactatttttttatataaactaacttcttttct-gcagAGCATGCGCAGGATGTCACAGAGAGATTGGTCACGGGCGTTTTCTCAGTTGCATGGGAGCTGTTTGGCATCCGGAATGTTTTCGTTGCCATGCATGTAGT
| | || | | |||| | || | | | | || | | || ||| | | | || | | | || |||||| | || ||| | || || || ||||| || || || | ||||| ||||||||||| | ||||||||||| |||||||| ||||| |||||||| |
gtaaatggttcaaaaatacattaatgtccatttcttagattttcagacactatcatctctagatagtgatatgatgcatgatcacattagctccaatgagtcaattttgtttctttgtttattttcttggagGATATGTGTCGGTTGCCAAGCTGAGATAGGACATGGAAGGTTTCTGAGTTGCATGGGTGGCGTTTGGCATCCTGAATGTTTCTGTTGCAATGCATGTGAT
upper sequence: GRMZM2G017845_T04 (Zea mays), 3'ss of exon 4
lower sequence: Vv04s0023g01040.t01 (Vitis vinifera), 3'ss of exon 8
gtaatgctcaagaacacaccaggatgattggcatggaag-atatcattttgaccttttttctcttactatttttttatataaactaact-tcttttctgcagAGCATGCGCAGGATGTCACAGAGAGATTGGTCACGGGCGTTTTCTCAGTTGCATGGGAGCTGTTTGGCATCCGGAATGTTTTCGTTGCCATGCATGTAGT
| || | | || | ||| ||| |||| ||| | | | | | | | || | || | | || || || || | || || || |||||||| | | | | || ||||||| |||||||||||||| |||||||||||||| ||||| ||| ||
-tcataaatg-gtgcttctcatattttttgtcattttcctgcatcagtttcatagacatcatatgaaacctcacatggatgattacacaataccatttgtagGATCTGTGCTCGGTGCAACCTTGAAATTGGTCATGAAAGACATTTGAGGCGCATGGGTGCTGTTTGGCATCCAGAATGTTTTCGTTGTCATGCTTGTGGT
upper sequence: GRMZM2G017845_T04 (Zea mays), 3'ss of exon 4
lower sequence: Vv04s0023g01030.t01 (Vitis vinifera), 3'ss of exon 5
gtaatgctcaagaacacaccaggatgattggcatg-----gaagatatcattttgaccttttttctcttactatttttttatataaactaacttcttttctgcagAGCATGCGCAGGATGTCACAGAGAGATTGGTCACGGGCGTTTTCTCAGTTGCATGGGAGCTGTTTGGCATCCGGAATGTTTTCGTTGCCATGCATGTAGT
| || | | | || | | || ||| | | | | | ||| | | | | | ||| || || | | | || || || || || || || | ||||||||||| || | | | | ||||||||||| |||||||||||||| |||||||||||||||| ||| ||| |
-tgataaataggg-cttctcatgttttatgtcattctcctgcatgtgtgtcatggacttcgtatgagacctcacatggttaattacacaa---tatcacttgtagGATCTGTGCTGGGTGCAACTGCGAGATTGGTCATGGAAGATATTTGAGTTGCATGGGTGCTGTTTGGCATCCAGAATGTTTTCGTTGCCGTGCTTGTGGG
upper sequence: GRMZM2G017845_T04 (Zea mays), 3'ss of exon 4
lower sequence: Vv18s0001g11820.t01 (Vitis vinifera), 3'ss of exon 4
-------gtaatgctcaagaacaca-ccaggatgattggcatggaagatatcattttgaccttttttctcttactatttttttatataaactaacttcttttctgcagAGCATGCGCAGGATGTCACAGAGAGATTGGTCACGGGCGTTTTCTCAGTTGCATGGGAGCTGTTTGGCATCCGGAATGTTTTCGTTGCCATGCATGTAGT
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tctagttttctcattcaagattatttccctcatgaggaattttacaca-atcacaaggaacattatcaaataatgccctgtttctgta-------tttttttggatagGATCTGTGCTGGTTGCAATACTGAGATTGGTCATGGACGTTTTCTAAGTTGCATGGGTGCAGTTTGGCATCCAGAATGTTTCAGATGCCACGGTTGCGGCMapped EST sequences
Showing partial alignments of ESTs and genomic sequences. See full alignments
ATGC EST sequence
ATGC genomic sequence (exon)
ATGC genomic sequence (truncated intron)
EST:
gi|31355012|gb|CD439369.1|CD439369EST: GGTGGAAATGCATATCACCCATTACCATTTATGTTCTCATCTGGATTCAG AGCATGCGCAGGATGTCACAGAGAGATTGGTCACGGGCGTTTTCTCAGTTG
genomic: GGTGGAAATGCATATCACCCATTACCATTTATGTTCTCATCTGGATTCAGgttcatttca ... ttttctgcagAGCATGCGCAGGATGTCACAGAGAGATTGGTCACGGGCGTTTTCTCAGTTG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttttgaccttttttctcttactatttttttatataaactaacttcttttctgcagAGCATGCGCAGGATGTCACAGAGAGATTGGTCACGGGCGTTTTCTCAGTTGCATGGGAGCTGTTTGGCATCCGGAATGTTTTCGTTGCCATGCATGTAGT
aactaac putative branch site (score: 1)
ctaacttcttttct CT-rich tract
ttttttctcttactat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaatgctcaagaacacaccaggatgattggcatggaagatatcattttgaccttttttctcttactatttttttatataaactaacttcttttctgcagAGCATGCGCAGGATGTCACAGAGAGATTGGTCACGGGCGTTTTCTCAGTTGCATGGGAGCTGTTTGGCATCCGGAATGTTTTCGTTGCCATGCATGTAGT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT