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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TACAGAACATAACAATGTCCCAAGCTCAAACAGTGATTCTGTTATGGCTGAAGGAGAACCTGCCTCAAATGCTGCTGCTGGTGACAAAGAACAACCAAAGgtattatcactgtccataagttacaaactaaaaatgccctaacctgtctccaatacttgaagttttagcagttgcatgtactcatgaactcttctctgtg...

Basic information

species Zea mays
transcript GRMZM2G165926_T02
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G165926_T02 (Zea mays), 5'ss of exon 6
lower sequence: LOC_Os03g13970.1 (Oryza sativa), 5'ss of exon 6
TACAGAACATAACAATGTCCCAAGCTCAAACAGTGATTCTGTTATGGCTGAAGGAGAACCTGCCTCAAATGCTGCTGCTGGTGACAAAGAACAACCAAAGgtattatcactgtccataagttacaaacta-aaaatgccctaacctgtctccaatacttgaagttttagcagttgcatgtactcatgaactcttctctgtg
|  | |  |  || ||| | |||||||||||  ||||||||||||||| ||||  |||||||||||||||||||||| || | | ||||| || || |||||||| ||  | |||   |||||   |  | |   ||       ||            | | ||  ||  || |   |  |    |  |  ||||      
TGAAAATAAGGACCATGCCTCAAGCTCAAACGCTGATTCTGTTATGGCAGAAGCGGAACCTGCCTCAAATGCTGCTGATGATAAAAAAGATCAGCCGAAGgtattgtcgttatcctacagttaatcatcacattgtgaaaagttctacaattggggtattatgtcata-tagctatctaaatcattttaaacttcatcaac
















Mapped 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|37380959|gb|CF627330.1|CF627330
EST:     GCTGCTGGTGACAAAGAACAACCAAAG                         GATGATGACGATCTACTACAGCAGGCACTTGCAATGTCAATGGAGGGTGGT
genomic: GCTGCTGGTGACAAAGAACAACCAAAGgtattatcac ... gtgatcacagGATGATGACGATCTACTACAGCAGGCACTTGCAATGTCAATGGAGGGTGGT
EST: gi|18162870|gb|BM332709.1|BM332709
EST:     AAGGAGAACCTGCCTCAAATGCTGCTGCTGGTGACAAAGAACAACCAAAG                         GATGATGACGATCTACTACAGCAGGCACTTGCAATGTCAATGGAGGGTGGT
genomic: AAGGAGAACCTGCCTCAAATGCTGCTGCTGGTGACAAAGAACAACCAAAGgtattatcac ... gtgatcacagGATGATGACGATCTACTACAGCAGGCACTTGCAATGTCAATGGAGGGTGGT
EST: gi|5525732|gb|AI861625.1|AI861625
EST:     AAGGAGAACCTGCCTCAAATGCTGCTGCTGGTGACAAAGAACAACCAAAG                         GATGATGACGATCTACTACAGCAGGCACTTGCAATGTCAATGGAGGGTGGT
genomic: AAGGAGAACCTGCCTCAAATGCTGCTGCTGGTGACAAAGAACAACCAAAGgtattatcac ... gtgatcacagGATGATGACGATCTACTACAGCAGGCACTTGCAATGTCAATGGAGGGTGGT
EST: gi|71419000|gb|DR804613.1|DR804613
EST:     AAGGAGAACCTGCCTCAAATGCTGCTGCTGGTGACAAAGAACAACCAAAG                         GATGATGACGATCTACTACAGCAGGCACTTGCAATGTCAATGGAGGGTGGT
genomic: AAGGAGAACCTGCCTCAAATGCTGCTGCTGGTGACAAAGAACAACCAAAGgtattatcac ... gtgatcacagGATGATGACGATCTACTACAGCAGGCACTTGCAATGTCAATGGAGGGTGGT
EST: gi|13237368|gb|BG355382.1|BG355382
EST:     AAGGAGAACCTGCCTCAAATGCTGCTGCTGGTGACAAAGAACAACCAAAG                         GATGATGACGATCTACTACAGCA
genomic: AAGGAGAACCTGCCTCAAATGCTGCTGCTGGTGACAAAGAACAACCAAAGgtattatcac ... gtgatcacagGATGATGACGATCTACTACAGCA
EST: gi|84977035|gb|DW475457.1|DW475457
EST:     GGAGAACCTTGCCTCAAATGCTTGCTGCTGGTGACAAAGAACAACCAAAG                         GATGATGACCGATCTACTTACAGCAGGCACTTGCAATGTCAATGGAGG-TG
genomic: GGAGAACCT-GCCTCAAATGCT-GCTGCTGGTGACAAAGAACAACCAAAGgtattatcac ... gtgatcacagGATGATGAC-GATCTACT-ACAGCAGGCACTTGCAATGTCAATGGAGGGTG
EST: gi|60337128|gb|DN204101.1|DN204101
EST:     AAGGAGAACCTGCCTCAAATGCTGCTGCTGGTGACAAAGAACAACCAAAG                         GATGATGACGATCTACTACAGCAGGCACTTGCAATGTCAATGGAGGGTGGT
genomic: AAGGAGAACCTGCCTCAAATGCTGCTGCTGGTGACAAAGAACAACCAAAGgtattatcac ... gtgatcacagGATGATGACGATCTACTACAGCAGGCACTTGCAATGTCAATGGAGGGTGGT
EST: gi|60353359|gb|DN220332.1|DN220332
EST:     AAGGAGAACCTGCCTCAAATGCTGCTGCTGGTGACAAAGAACAACCAAAG                         GATGATGACGATCTACTACAGCAGGCACTTGCAATGTCAATGGAGGGTGGT
genomic: AAGGAGAACCTGCCTCAAATGCTGCTGCTGGTGACAAAGAACAACCAAAGgtattatcac ... gtgatcacagGATGATGACGATCTACTACAGCAGGCACTTGCAATGTCAATGGAGGGTGGT
EST: gi|60347266|gb|DN214239.1|DN214239
EST:     AAGGAGAACCTGCCTCAAATGCTGCTGCTGGTGACAAAGAACAACCAAAG                         GATGATGACGATCTACTACAGCAGGCACTTGCAATGTCAATGGAGGGTGGT
genomic: AAGGAGAACCTGCCTCAAATGCTGCTGCTGGTGACAAAGAACAACCAAAGgtattatcac ... gtgatcacagGATGATGACGATCTACTACAGCAGGCACTTGCAATGTCAATGGAGGGTGGT
EST: gi|31664308|gb|CD573033.1|CD573033
EST:     CAAATGCTGCTGCTGGTGACAAAGAACANCCAAAG                         GATGATGACGATCTACTACAGCAGGCACTTGCAATGTCAATGGAGGGTGGT
genomic: CAAATGCTGCTGCTGGTGACAAAGAACAACCAAAGgtattatcac ... gtgatcacagGATGATGACGATCTACTACAGCAGGCACTTGCAATGTCAATGGAGGGTGGT
EST: gi|261490449|gb|GO359940.1|GO359940
EST:     AAGGAGAACCTGCCTCAAATGCTGCTGCTGGTGACAAAGAACAACCAAAG                         GATGATGACGATCTACTACAGCAGGCACTTGCAATGTCAATGGAGGGTGGT
genomic: AAGGAGAACCTGCCTCAAATGCTGCTGCTGGTGACAAAGAACAACCAAAGgtattatcac ... gtgatcacagGATGATGACGATCTACTACAGCAGGCACTTGCAATGTCAATGGAGGGTGGT
EST: gi|60349443|gb|DN216416.1|DN216416
EST:     AAGGAGAACCTGCCTCAAATGCTGCTGCTGGTGACAAAGAACAACCAAAG                         GATGATGACGATCTACTACAGCAGGCACTTGCAATGTCAATGGAGGGTGGT
genomic: AAGGAGAACCTGCCTCAAATGCTGCTGCTGGTGACAAAGAACAACCAAAGgtattatcac ... gtgatcacagGATGATGACGATCTACTACAGCAGGCACTTGCAATGTCAATGGAGGGTGGT
EST: gi|60346958|gb|DN213931.1|DN213931
EST:     AAGGAGAACCTGCCTCAAATGCTGCTGCTGGTGACAAAGAACAACCAAAG                         GATGATGACGATCTACTACAGCAGGCACTTGCAATGTCAATGGAGGGTGGT
genomic: AAGGAGAACCTGCCTCAAATGCTGCTGCTGGTGACAAAGAACAACCAAAGgtattatcac ... gtgatcacagGATGATGACGATCTACTACAGCAGGCACTTGCAATGTCAATGGAGGGTGGT
EST: gi|18174967|gb|BM350355.1|BM350355
EST:     AAGGAGAACCTGCCTCAAATGCTGCTGCTGGTGACAAAGAACAACCAAAG                         GATGATGACGATCTACTACAGCAGGCACTTGCAATGTCAATGGAGGGTGGT
genomic: AAGGAGAACCTGCCTCAAATGCTGCTGCTGGTGACAAAGAACAACCAAAGgtattatcac ... gtgatcacagGATGATGACGATCTACTACAGCAGGCACTTGCAATGTCAATGGAGGGTGGT
EST: gi|67025094|gb|CO453843.1|CO453843
EST:     AGGAGA-CCTGCCTNCAA-TGCTGCTGCTGGTGACAA-GAACAACCAA-G                         GATGATGACGATCTACTACAGCAGGCACTTGCAATGTCAATGGAGGGTGGT
genomic: AGGAGAACCTGCCT-CAAATGCTGCTGCTGGTGACAAAGAACAACCAAAGgtattatcac ... gtgatcacagGATGATGACGATCTACTACAGCAGGCACTTGCAATGTCAATGGAGGGTGGT
EST: gi|60357544|gb|DN224517.1|DN224517
EST:     AAGGAGAACCTGCCTCAAATGCTGCTGCTGGTGACAAAGAACAACCAAAG                         GATGATGACGATCTACTACAGCAGGCACTTGCAATGTCAATGGAGGGTGGT
genomic: AAGGAGAACCTGCCTCAAATGCTGCTGCTGGTGACAAAGAACAACCAAAGgtattatcac ... gtgatcacagGATGATGACGATCTACTACAGCAGGCACTTGCAATGTCAATGGAGGGTGGT
EST: gi|60354620|gb|DN221593.1|DN221593
EST:     AAGGAGAACCTGCCTCAAATGCTGCTGCTGGTGACAAAGAACAACCAAAG                         GATGATGACGATCTACTACAGCAGGCACTTGCAATGTCAATGGAGGGTGGT
genomic: AAGGAGAACCTGCCTCAAATGCTGCTGCTGGTGACAAAGAACAACCAAAGgtattatcac ... gtgatcacagGATGATGACGATCTACTACAGCAGGCACTTGCAATGTCAATGGAGGGTGGT
EST: gi|44901350|gb|CK827895.1|CK827895
EST:     AAGGAGAACCTGCCTCAAATGCTGCTGCTGGTGACAAAGAACAACCAAAG                         GATGATGACGATCTACTACAGCAGGCACTTGCAATGTCAATGGAGGGTGGT
genomic: AAGGAGAACCTGCCTCAAATGCTGCTGCTGGTGACAAAGAACAACCAAAGgtattatcac ... gtgatcacagGATGATGACGATCTACTACAGCAGGCACTTGCAATGTCAATGGAGGGTGGT
EST: gi|60399456|gb|DN232268.1|DN232268
EST:     AAGGAGAACCTGCCTCAAATGCTGCTGCTGGTGACAAAGAACAACCAAAG                         GATGATGACGATCTACTACAGCAGGCACTTGCAATGTCAATGGAGGGTGGT
genomic: AAGGAGAACCTGCCTCAAATGCTGCTGCTGGTGACAAAGAACAACCAAAGgtattatcac ... gtgatcacagGATGATGACGATCTACTACAGCAGGCACTTGCAATGTCAATGGAGGGTGGT
EST: gi|38502551|gb|CF972411.1|CF972411
EST:     AAGGAGAACCTGCCTCAAATGCTGCTGCTGGTGACAAAGAACAACCAAAG                         GATGATGACGATCTACTACAGCAGGCACTTGCAATGTCAATGGAGGGTGGT
genomic: AAGGAGAACCTGCCTCAAATGCTGCTGCTGGTGACAAAGAACAACCAAAGgtattatcac ... gtgatcacagGATGATGACGATCTACTACAGCAGGCACTTGCAATGTCAATGGAGGGTGGT
EST: gi|32930239|gb|CF035051.1|CF035051
EST:     AAGGAGAACCTGCCTCAAATGCTGCTGCTGGTGACAAAGAACAACCAAAG                         GATGATGACGATCTACTACAGCAGGCACTTGCAATGCCAATGGAGGGTGGT
genomic: AAGGAGAACCTGCCTCAAATGCTGCTGCTGGTGACAAAGAACAACCAAAGgtattatcac ... gtgatcacagGATGATGACGATCTACTACAGCAGGCACTTGCAATGTCAATGGAGGGTGGT

RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 4 RNA-Seq libraries.


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 195

TACAGAACATAACAATGTCCCAAGCTCAAACAGTGATTCTGTTATGGCTGAAGGAGAACCTGCCTCAAATGCTGCTGCTGGTGACAAAGAACAACCAAAGgtattatcac ... gtgatcacagGATGATGACGATCTACTACAGCAGGCACTTGCAATGTCAATGGAGGGTGGTGCTTCAGGATCTGCAGCTGTGACTGACTCTGCTATGGCAGAAGCTGGTG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 238

TACAGAACATAACAATGTCCCAAGCTCAAACAGTGATTCTGTTATGGCTGAAGGAGAACCTGCCTCAAATGCTGCTGCTGGTGACAAAGAACAACCAAAGgtattatcac ... gtgatcacagGATGATGACGATCTACTACAGCAGGCACTTGCAATGTCAATGGAGGGTGGTGCTTCAGGATCTGCAGCTGTGACTGACTCTGCTATGGCAGAAGCTGGTG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 218

TACAGAACATAACAATGTCCCAAGCTCAAACAGTGATTCTGTTATGGCTGAAGGAGAACCTGCCTCAAATGCTGCTGCTGGTGACAAAGAACAACCAAAGgtattatcac ... gtgatcacagGATGATGACGATCTACTACAGCAGGCACTTGCAATGTCAATGGAGGGTGGTGCTTCAGGATCTGCAGCTGTGACTGACTCTGCTATGGCAGAAGCTGGTG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 232

TACAGAACATAACAATGTCCCAAGCTCAAACAGTGATTCTGTTATGGCTGAAGGAGAACCTGCCTCAAATGCTGCTGCTGGTGACAAAGAACAACCAAAGgtattatcac ... gtgatcacagGATGATGACGATCTACTACAGCAGGCACTTGCAATGTCAATGGAGGGTGGTGCTTCAGGATCTGCAGCTGTGACTGACTCTGCTATGGCAGAAGCTGGTG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TACAGAACATAACAATGTCCCAAGCTCAAACAGTGATTCTGTTATGGCTGAAGGAGAACCTGCCTCAAATGCTGCTGCTGGTGACAAAGAACAACCAAAGgtattatcactgtccataagttacaaactaaaaatgccctaacctgtctccaatacttgaagttttagcagttgcatgtactcatgaactcttctctgtg

- - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - -  AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - actaaaaa