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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaattgggtcgcctatctattaccgacactgttgagctgctaaagattattctttggttaacgttgtgttttttgttgggcagTTTTTGTTTTGTTCATGGTACTGAACTCACACCAGATGTCTCCCAATCTTTTG

Basic information

species Zea mays
transcript GRMZM2G492252_T01
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G492252_T01 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os03g16570.1 (Oryza sativa), 3'ss of exon 2
gtaattgggtcg---cctatctattaccgacactgttgagctgctaaagat---tattctttggttaacgttgtgt----tttttgttgggcagTTTTTGTTTTGTTCATGGTACTGAACTCACACCAGATGTCTCCCAATCTTTTG
|||||  || |    ||| | || |||||| | | || |||||  ||| ||    ||| | | ||||| |   | |    || || |||||||||| || | ||||||||||||||||||||||||||||||||||| ||  |||||
gtaatgtgggcatgccctttgtactaccgatattattaagctgtaaaaaatatcgattttctagttaatgcgatctattattctttttgggcagTTCTTATGTTGTTCATGGTACTGAACTCACACCAGATGTCTCCGAACTTTTTG
















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|211128948|gb|FL128226.1|FL128226
EST:     TGCAGGGAGCAGGCCGGTGAATAGCAATTCCTTGGTTTTTCTTCTAACTG                         TTTTTGTTTTGTTCATGGTACTGAACTCACACCAGATGTCTCCCAATCTTT
genomic: TGCAGGGAGCAGGCCGGTGAATAGCAATTCCTTGGTTTTTCTTCTAACTGgtaattgggt ... tgttgggcagTTTTTGTTTTGTTCATGGTACTGAACTCACACCAGATGTCTCCCAATCTTT
EST: gi|211128945|gb|FL128223.1|FL128223
EST:     TGCANGGAGCAGGCCGGTGAATAGCAATTCCTTGGTTTTTCTTCTAACTG                         TTTTTGTTTTGTTCATGGTACTGAACTCACACCAGATGTCTCCCAATCTTT
genomic: TGCAGGGAGCAGGCCGGTGAATAGCAATTCCTTGGTTTTTCTTCTAACTGgtaattgggt ... tgttgggcagTTTTTGTTTTGTTCATGGTACTGAACTCACACCAGATGTCTCCCAATCTTT
EST: gi|149105940|gb|EE291566.2|EE291566
EST:     TGCAGGGAGCAGGCCGGTGAATAGCAATTCCTTGGTTTTTCTTCTAACTG                         TTTTTGTTTTGTTCATGGTACTGAACTCACACCAGATGTCTCCCAATCTTT
genomic: TGCAGGGAGCAGGCCGGTGAATAGCAATTCCTTGGTTTTTCTTCTAACTGgtaattgggt ... tgttgggcagTTTTTGTTTTGTTCATGGTACTGAACTCACACCAGATGTCTCCCAATCTTT
EST: gi|88758241|gb|DY542382.1|DY542382
EST:     TGCAGGGAGCAGGCCGGTGAATAGCAATTCCTTGGTTTTTCTTCTAACTG                         TTTTTGTTTTGTTCATGGTACTGAACTCACACCAGATGTCTCCCAATCTTT
genomic: TGCAGGGAGCAGGCCGGTGAATAGCAATTCCTTGGTTTTTCTTCTAACTGgtaattgggt ... tgttgggcagTTTTTGTTTTGTTCATGGTACTGAACTCACACCAGATGTCTCCCAATCTTT
EST: gi|71424496|gb|DR806334.1|DR806334
EST:     TGCAGGGAGCAGGCCGGTGAATAGCAATTCCTTGGTTTTTCTTCTAACTG                         TTTTTGTTTTGTTCATGGTACTGAACTCACACCAGATGTCTCCCAATCTTT
genomic: TGCAGGGAGCAGGCCGGTGAATAGCAATTCCTTGGTTTTTCTTCTAACTGgtaattgggt ... tgttgggcagTTTTTGTTTTGTTCATGGTACTGAACTCACACCAGATGTCTCCCAATCTTT
EST: gi|211129864|gb|FL128228.1|FL128228
EST:     GCCAGGGAGCAGGCCGGTGAATAGCAATTCCTTGGTTTT-CTTCTAACTG                         TTTTTTGTTTTGTTCATGGTACTGAACCCACACCAGATGTCTCCCAATCTT
genomic: GC-AGGGAGCAGGCCGGTGAATAGCAATTCCTTGGTTTTTCTTCTAACTGgtaattgggt ... tgttgggcagTTTTT-GTTTTGTTCATGGTACTGAACTCACACCAGATGTCTCCCAATCTT
EST: gi|211129863|gb|FL128227.1|FL128227
EST:     TGCAGGGAGCAGGCCGGTGAATAGCAATTCCTTGGTTTTTCTTCTAACTG                         TTTTTGTTTTGTTCATGGTACTGAACTCACACCAGATGTCTCCCAATCTTT
genomic: TGCAGGGAGCAGGCCGGTGAATAGCAATTCCTTGGTTTTTCTTCTAACTGgtaattgggt ... tgttgggcagTTTTTGTTTTGTTCATGGTACTGAACTCACACCAGATGTCTCCCAATCTTT
EST: gi|37417624|gb|CF646466.1|CF646466
EST:     TGCAGGGAGCAGGCCGGTGAATAGCAATTCCTTGGTTTTTCTTCTAACTG                         TTTTTGTTTTGTTCATGGTACTGAACTCACACCAGATGTCTCCCAATCTTT
genomic: TGCAGGGAGCAGGCCGGTGAATAGCAATTCCTTGGTTTTTCTTCTAACTGgtaattgggt ... tgttgggcagTTTTTGTTTTGTTCATGGTACTGAACTCACACCAGATGTCTCCCAATCTTT
EST: gi|50324565|gb|CO519691.1|CO519691
EST:     TGCAGGGAGCAGGCCGGTGAATAGCAATTCCTTGGTTTTTCTTCTAACTG                         TTTTTGTTTTGTTCATGGTACTGAACTCACACCAGATGTCTCCCAATCTTT
genomic: TGCAGGGAGCAGGCCGGTGAATAGCAATTCCTTGGTTTTTCTTCTAACTGgtaattgggt ... tgttgggcagTTTTTGTTTTGTTCATGGTACTGAACTCACACCAGATGTCTCCCAATCTTT
EST: gi|71774882|gb|DR972760.1|DR972760
EST:     TGCAGGGAGCAGGCCGGTGAATAGCAATTCCTTGGTTTTTCTTCTAACTG                         TTTTTGTTTTGTTCATGGTACTGAACTCACACCAGATGTCTCCCAATCTTT
genomic: TGCAGGGAGCAGGCCGGTGAATAGCAATTCCTTGGTTTTTCTTCTAACTGgtaattgggt ... tgttgggcagTTTTTGTTTTGTTCATGGTACTGAACTCACACCAGATGTCTCCCAATCTTT
EST: gi|91868647|gb|EB400100.1|EB400100
EST:     TGCAGGGAGCAGGCCGGTGAATAGCAATTCCTTGGTTTTTCTTCTAACTG                         TTTTTGTTTTGTTCATGGTACTGAACTCACACCAGATGTCTCCCAATCTTT
genomic: TGCAGGGAGCAGGCCGGTGAATAGCAATTCCTTGGTTTTTCTTCTAACTGgtaattgggt ... tgttgggcagTTTTTGTTTTGTTCATGGTACTGAACTCACACCAGATGTCTCCCAATCTTT
EST: gi|71426202|gb|DR807252.1|DR807252
EST:     TGCAGGGAGCAGGCCGGTGAATAGCAATTCCTTGGTTTTTCTTCTAACTG                         TTTTTGTTTTGTTCATGGTACTGAACTCACACCAGATGTCTCCCAATCTTT
genomic: TGCAGGGAGCAGGCCGGTGAATAGCAATTCCTTGGTTTTTCTTCTAACTGgtaattgggt ... tgttgggcagTTTTTGTTTTGTTCATGGTACTGAACTCACACCAGATGTCTCCCAATCTTT
EST: gi|211129866|gb|FL128230.1|FL128230
EST:     TGCAGGGAGCAGGCCGGTGAATAGCAATTCCTTGGTTTTTCTTCTAACTG                         TTTTTGTTTTGTTCATGGTACTGAACTCACACCAGATGTCTCCCAATCTTT
genomic: TGCAGGGAGCAGGCCGGTGAATAGCAATTCCTTGGTTTTTCTTCTAACTGgtaattgggt ... tgttgggcagTTTTTGTTTTGTTCATGGTACTGAACTCACACCAGATGTCTCCCAATCTTT
EST: gi|211128943|gb|FL128221.1|FL128221
EST:     TGCAGGGAGCAGGCCGGTGAATAGCAATTCCTTGGTTTTTCTTCTAACTG                         TTTTTGTTTTGTTCATGGTACTGAACTCACACCAGATGTCTCCCAATCTTT
genomic: TGCAGGGAGCAGGCCGGTGAATAGCAATTCCTTGGTTTTTCTTCTAACTGgtaattgggt ... tgttgggcagTTTTTGTTTTGTTCATGGTACTGAACTCACACCAGATGTCTCCCAATCTTT
EST: gi|211129865|gb|FL128229.1|FL128229
EST:     TGCAGGGAGCAGGCCGGTGAATAGCAATTCCTTGGTTTTTCTTCTAACTG                         TTTTTGTTTTGTTCATGGTACTGAACTCACACCAGATGTCTCCCAATCTTT
genomic: TGCAGGGAGCAGGCCGGTGAATAGCAATTCCTTGGTTTTTCTTCTAACTGgtaattgggt ... tgttgggcagTTTTTGTTTTGTTCATGGTACTGAACTCACACCAGATGTCTCCCAATCTTT
EST: gi|211039435|gb|FL384655.1|FL384655
EST:     TGCAGGGAGCAGGCCGGTGAATAGCAATTCCTTGGTTTTTCTTCTAACTG                         TTTTTGTTTTGTTCATGGTACTGAACTCACACCAGATGTCTCCCAATCTTT
genomic: TGCAGGGAGCAGGCCGGTGAATAGCAATTCCTTGGTTTTTCTTCTAACTGgtaattgggt ... tgttgggcagTTTTTGTTTTGTTCATGGTACTGAACTCACACCAGATGTCTCCCAATCTTT
EST: gi|211252415|gb|FL420141.1|FL420141
EST:     TGCAGGGAGCAGGCCGGTGAATAGCAATTCCTTGGTTTTTCTTCTAACTG                         TTTTTGTTTTGTTCATGGTACTGAACTCACACCAGATGTCTCCCAATCTTT
genomic: TGCAGGGAGCAGGCCGGTGAATAGCAATTCCTTGGTTTTTCTTCTAACTGgtaattgggt ... tgttgggcagTTTTTGTTTTGTTCATGGTACTGAACTCACACCAGATGTCTCCCAATCTTT
EST: gi|89760191|gb|DY688711.1|DY688711
EST:     TGCAGGGAGCAGGCCGGTGAATAGCAATTCCTTGGTTTTTCTTCTAACTG                         TTTTTGTTTTGTTCATGGTACTGAACTCACACCAGATGTCTCCCAATCTTT
genomic: TGCAGGGAGCAGGCCGGTGAATAGCAATTCCTTGGTTTTTCTTCTAACTGgtaattgggt ... tgttgggcagTTTTTGTTTTGTTCATGGTACTGAACTCACACCAGATGTCTCCCAATCTTT
EST: gi|211005956|gb|FL398095.1|FL398095
EST:     TGCAGGGAGCAGGCCGGTGAATAGCAATTCCTTGGTTTTTCTTCTAACTG                         TTTTTGTTTTGTTCATGGTACTGAACTCACACCAGATGTCTCCCAATCTTT
genomic: TGCAGGGAGCAGGCCGGTGAATAGCAATTCCTTGGTTTTTCTTCTAACTGgtaattgggt ... tgttgggcagTTTTTGTTTTGTTCATGGTACTGAACTCACACCAGATGTCTCCCAATCTTT
EST: gi|148971543|gb|EE022249.2|EE022249
EST:     TGCAGGGAGCAGGCCGGTGAATAGCAATTCCTTGGTTTTTCTTCTAACTG                         TTTTTGTTTTGTTCATGGTACTGAACTCACACCAGATGTCTCCCAATCTTT
genomic: TGCAGGGAGCAGGCCGGTGAATAGCAATTCCTTGGTTTTTCTTCTAACTGgtaattgggt ... tgttgggcagTTTTTGTTTTGTTCATGGTACTGAACTCACACCAGATGTCTCCCAATCTTT
EST: gi|93014828|gb|EB640348.1|EB640348
EST:     TGCAGGGAGCAGGCCGGTGAATAGCAATTCCTTGGTTTTTCTTCTAACTG                         TTTTTGTTTTGTTCATGGTACTGAACTCACACCAGATGTCTCCCAATCTTT
genomic: TGCAGGGAGCAGGCCGGTGAATAGCAATTCCTTGGTTTTTCTTCTAACTGgtaattgggt ... tgttgggcagTTTTTGTTTTGTTCATGGTACTGAACTCACACCAGATGTCTCCCAATCTTT
EST: gi|211045933|gb|FL419469.1|FL419469
EST:     TGCAGGGAGCAGGCCGGTGAATAGCAATTCCTTGGTTTTTCTTCTAACTG                         TTTTTGTTTTGTTCATGGTACTGAACTCACACCAGATGTCTCCCAATCTTT
genomic: TGCAGGGAGCAGGCCGGTGAATAGCAATTCCTTGGTTTTTCTTCTAACTGgtaattgggt ... tgttgggcagTTTTTGTTTTGTTCATGGTACTGAACTCACACCAGATGTCTCCCAATCTTT
EST: gi|211128939|gb|FL128217.1|FL128217
EST:     TGCAGGGAGCAGGCCGGTGAATAGCAATTCCTTGGTTTTTCTTCTAACTG                         TTTTTGTTTTGTTCATGGTACTGAACTCACACCAGATGTCTCCCAATCTTT
genomic: TGCAGGGAGCAGGCCGGTGAATAGCAATTCCTTGGTTTTTCTTCTAACTGgtaattgggt ... tgttgggcagTTTTTGTTTTGTTCATGGTACTGAACTCACACCAGATGTCTCCCAATCTTT
EST: gi|211128947|gb|FL128225.1|FL128225
EST:     TGCAGGGAGCAGGCCGGTGAATAGCAATTCCTTGGTTTTTCTTCTAACTG                         TTTTTGTTTTGTACATGGTACTGAACTCACACC
genomic: TGCAGGGAGCAGGCCGGTGAATAGCAATTCCTTGGTTTTTCTTCTAACTGgtaattgggt ... tgttgggcagTTTTTGTTTTGTTCATGGTACTGAACTCACACC
EST: gi|211128941|gb|FL128219.1|FL128219
EST:     TGCAGGGAGCAGGCCGGTGAATAGCAATTCCTTGGTTTTTCTTCTAACTG                         TTTTTGTTTTGTTCATGGTACTGAACTCACACCAGATGTCTCCCAATCTTT
genomic: TGCAGGGAGCAGGCCGGTGAATAGCAATTCCTTGGTTTTTCTTCTAACTGgtaattgggt ... tgttgggcagTTTTTGTTTTGTTCATGGTACTGAACTCACACCAGATGTCTCCCAATCTTT
EST: gi|211128940|gb|FL128218.1|FL128218
EST:     TGCAGGGAGCAGGCCGGTGAATAGCAATTCCTTGGTTTTTCTTCTAACTG                         TTTTTGTTTTGTTCATGGTACTGAACTCACACCAGATGTCTCCCAATCTTT
genomic: TGCAGGGAGCAGGCCGGTGAATAGCAATTCCTTGGTTTTTCTTCTAACTGgtaattgggt ... tgttgggcagTTTTTGTTTTGTTCATGGTACTGAACTCACACCAGATGTCTCCCAATCTTT
EST: gi|76936255|gb|DV174660.1|DV174660
EST:     TGCAGGGAGCAGGCCGGTGAATAGCAATTCCTTGGTTTTTCTTCTAACTG                         TTTTTGTTTTGTTCATGGTACTGAACTCACACCAGATGTCTCCCAATCTTT
genomic: TGCAGGGAGCAGGCCGGTGAATAGCAATTCCTTGGTTTTTCTTCTAACTGgtaattgggt ... tgttgggcagTTTTTGTTTTGTTCATGGTACTGAACTCACACCAGATGTCTCCCAATCTTT

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: 47 (upstream exon), 46 (downstream exon)
Score: 51

CGAATTCATGCAGGGAGCAGGCCGGTGAATAGCAATTCCTTGGTTTTTCTTCTAACTGgtaattgggt ... tgttgggcagTTTTTGTTTTGTTCATGGTACTGAACTCACACCAGATGTCTCCCAATCTTTTG


Block sizes: 25 (upstream exon), 48 (downstream exon)
Score: 4

CGAATTCATGCAGGGAGCAGGCCGGTGAATAGCAATTCCTTGGTTTTTCTTCTAACTGgtaattgggt ... tgttgggcagTTTTTGTTTTGTTCATGGTACTGAACTCACACCAGATGTCTCCCAATCTTTTG


Block sizes: 43 (upstream exon), 48 (downstream exon)
Score: 28

CGAATTCATGCAGGGAGCAGGCCGGTGAATAGCAATTCCTTGGTTTTTCTTCTAACTGgtaattgggt ... tgttgggcagTTTTTGTTTTGTTCATGGTACTGAACTCACACCAGATGTCTCCCAATCTTTTG


Block sizes: 49 (upstream exon), 26 (downstream exon)
Score: 8

CGAATTCATGCAGGGAGCAGGCCGGTGAATAGCAATTCCTTGGTTTTTCTTCTAACTGgtaattgggt ... tgttgggcagTTTTTGTTTTGTTCATGGTACTGAACTCACACCAGATGTCTCCCAATCTTTTG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctgttgagctgctaaagattattctttggttaacgttgtgttttttgttgggcagTTTTTGTTTTGTTCATGGTACTGAACTCACACCAGATGTCTCCCAATCTTTTG
                                        ttttttgtt  CT-rich tract
            taaagattattcttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaattgggtcgcctatctattaccgacactgttgagctgctaaagattattctttggttaacgttgtgttttttgttgggcagTTTTTGTTTTGTTCATGGTACTGAACTCACACCAGATGTCTCCCAATCTTTTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGATG