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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttctttcttattgataaaatatctaggaaagacacttaaaagcctagataatgtcgtttcctcgttttccatgttattaaggttcatcttaaccatacagGCATCTAACTACTTTGGACGATGCTCTGATTCGTACGAAATGGATGAACTGCAAGAAAGCAATCTCTGAAGAAGTGGAAATTGTGAAACAGTTGGATGCT

Basic information

species Zea mays
transcript GRMZM2G017305_T01
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G017305_T01 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os01g49000.1 (Oryza sativa), 3'ss of exon 1
ttctttcttattgataaaatatctagga--aagacacttaaaagcctagataatgtcgtt-tcctcgtttt---ccatgttatta-aggttcatcttaaccatacagGCATCTAACTACTTTGGACGATGCTCTGATTCGTACGAAATGGATGAACTGCAAGAAAGCAATCTCTGAAGAAGTGGAAATTGTGAAACAGTTGGATGCT
       ||   | ||||| |   || |  |  | | || ||       | ||||   || ||||  | ||   |||| |||| | || |     |  |   | ||||||||||||||||||||| || ||||||||||| || |||||| ||||||| |||||||| |||| ||| ||||| ||||| ||||||||| ||||||||
-------ttgaaggtaaaacactgagtatgacaaaatttgaacataacaaaaatgcatttatccttatattgatccatattatgatagataagattcgattgtgcagGCATCTAACTACTTTGGATGACGCTCTGATTCGCACAAAATGGCTGAACTGTAAGAAAGCTATCTGTGATGAAGTAGAAATCGTGAAACAGCTGGATGCT
















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|211070974|gb|FL043062.1|FL043062
EST:     TACGACACCTCCATCATCTTCTTCGACGGCGCCATCGCCCAGATCAACAA                         GCATCTAACTACTTTGGACGATGCTCTGATTCGTACGAAATGGATGAACTG
genomic: TACGACACCTCCATCATCTTCTTCGACGGCGCCATCGCCCAGATCAACAAgtgagcttct ... aaccatacagGCATCTAACTACTTTGGACGATGCTCTGATTCGTACGAAATGGATGAACTG
EST: gi|211070973|gb|FL043061.1|FL043061
EST:     TACGACACCTCCATCATCTTCTTCGACGGCGCCATCGCCCAGATCAACAA                         GCATCTAACTACTTTGGACGATGCTCTGATTCGTACGAAATGGATGAACTG
genomic: TACGACACCTCCATCATCTTCTTCGACGGCGCCATCGCCCAGATCAACAAgtgagcttct ... aaccatacagGCATCTAACTACTTTGGACGATGCTCTGATTCGTACGAAATGGATGAACTG
EST: gi|211070972|gb|FL043060.1|FL043060
EST:     TACGACACCTCCATCATCTTCTTCGACGGCGCCATCGCCCAGATCAACAA                         GCATCTAACTACTTTGGACGATGCTCTGATTCGTACGAAATGGATGAACTG
genomic: TACGACACCTCCATCATCTTCTTCGACGGCGCCATCGCCCAGATCAACAAgtgagcttct ... aaccatacagGCATCTAACTACTTTGGACGATGCTCTGATTCGTACGAAATGGATGAACTG
EST: gi|211073708|gb|FL043072.1|FL043072
EST:     TACGACACCTCCATCATCTTCTTCGACGGCGCCATCGCCCAGATCAACAA                         GCATCTAACTACTTTGGACGATGCTCTGATTCGTACGAAATGGATGAACTG
genomic: TACGACACCTCCATCATCTTCTTCGACGGCGCCATCGCCCAGATCAACAAgtgagcttct ... aaccatacagGCATCTAACTACTTTGGACGATGCTCTGATTCGTACGAAATGGATGAACTG
EST: gi|71309355|gb|DR790966.1|DR790966
EST:     TACGACACCTCCATCATCTTCTTCGACGGCGCCATCGCCCAGATCAACAA                         GCATCTAACTACTTTGGACGATGCTCTGATTCGTACGAAATGGATGAACTG
genomic: TACGACACCTCCATCATCTTCTTCGACGGCGCCATCGCCCAGATCAACAAgtgagcttct ... aaccatacagGCATCTAACTACTTTGGACGATGCTCTGATTCGTACGAAATGGATGAACTG
EST: gi|211073706|gb|FL043070.1|FL043070
EST:     TACGACACCTCCATCATCTTCTTCGACGGCGCCATCGCCCAGATCAACAA                         GCATCTAACTACTTTGGACGATGCTCTGATTCGTACGAAATGGATGAACTG
genomic: TACGACACCTCCATCATCTTCTTCGACGGCGCCATCGCCCAGATCAACAAgtgagcttct ... aaccatacagGCATCTAACTACTTTGGACGATGCTCTGATTCGTACGAAATGGATGAACTG
EST: gi|32827953|gb|CD967631.1|CD967631
EST:     TACGACACCTCCATCATCTTCTTCGACGGCGCCATCGCCCAGATCAACAA                         GCATCTAACTACTTTGGACGATGCTCTGATTCGTACGAAATGGATGAACTG
genomic: TACGACACCTCCATCATCTTCTTCGACGGCGCCATCGCCCAGATCAACAAgtgagcttct ... aaccatacagGCATCTAACTACTTTGGACGATGCTCTGATTCGTACGAAATGGATGAACTG
EST: gi|37418936|gb|CF647141.1|CF647141
EST:     TACGACACCTCCATCATCTTCTTCGACGGCGCCATCGCCCAGATCAACAA                         GCATCTAACTACTTTGGACGATGCTCTGATTCGTACGAAATGGATGAACTG
genomic: TACGACACCTCCATCATCTTCTTCGACGGCGCCATCGCCCAGATCAACAAgtgagcttct ... aaccatacagGCATCTAACTACTTTGGACGATGCTCTGATTCGTACGAAATGGATGAACTG
EST: gi|149102571|gb|EE188232.2|EE188232
EST:     TACGACACCTCCATCATCTTCTTCGACGGCGCCATCGCCCAGATCAACAA                         GCATCTAACTACTTTGGACGATGCTCTGATTCGTACGAAATGGATGAACTG
genomic: TACGACACCTCCATCATCTTCTTCGACGGCGCCATCGCCCAGATCAACAAgtgagcttct ... aaccatacagGCATCTAACTACTTTGGACGATGCTCTGATTCGTACGAAATGGATGAACTG
EST: gi|148978737|gb|EE026296.2|EE026296
EST:     TACGACACCTCCATCATCTTCTTCGACGGCGCCATCGCCCAGATCAACAA                         GCATCTAACTACTTTGGACGATGCTCTGATTCGTACGAAATGGATGAACTG
genomic: TACGACACCTCCATCATCTTCTTCGACGGCGCCATCGCCCAGATCAACAAgtgagcttct ... aaccatacagGCATCTAACTACTTTGGACGATGCTCTGATTCGTACGAAATGGATGAACTG
EST: gi|32823303|gb|CD963025.1|CD963025
EST:     TACGACACCTCCATCATCTTCTTCGACGGCGCCATCGCCCAGATCAACAA                         GCATCTAACTACTTTGGACGATGCTCTGATTCGTACGAAATGGATGAACTG
genomic: TACGACACCTCCATCATCTTCTTCGACGGCGCCATCGCCCAGATCAACAAgtgagcttct ... aaccatacagGCATCTAACTACTTTGGACGATGCTCTGATTCGTACGAAATGGATGAACTG
EST: gi|211073704|gb|FL043068.1|FL043068
EST:     TACGACACCTCCATCATCTTCTTCGACGGCGCCATCGCCCAGATCAACAA                         GCATCTAACTACTTTGGACGATGCTCTGATTCGTACGAAATGGATGAACTG
genomic: TACGACACCTCCATCATCTTCTTCGACGGCGCCATCGCCCAGATCAACAAgtgagcttct ... aaccatacagGCATCTAACTACTTTGGACGATGCTCTGATTCGTACGAAATGGATGAACTG
EST: gi|211073699|gb|FL043063.1|FL043063
EST:     TACGACACCTCCATCATCTTCTTCGACGGCGCCATCGCCCAGATCAACAA                         GCATCTAACTACTTTGGACGATGCTCTGATTCGTACGAAATGGATGAACTG
genomic: TACGACACCTCCATCATCTTCTTCGACGGCGCCATCGCCCAGATCAACAAgtgagcttct ... aaccatacagGCATCTAACTACTTTGGACGATGCTCTGATTCGTACGAAATGGATGAACTG
EST: gi|211073707|gb|FL043071.1|FL043071
EST:     TACGACACCTCCATCATCTTCTTCGACGGCGCCATCGCCCAGATCAACAA                         GCATCTAACTACTTTGGACGATGCTCTGATTCGTACGAAATGGATGAACTG
genomic: TACGACACCTCCATCATCTTCTTCGACGGCGCCATCGCCCAGATCAACAAgtgagcttct ... aaccatacagGCATCTAACTACTTTGGACGATGCTCTGATTCGTACGAAATGGATGAACTG
EST: gi|211070971|gb|FL043059.1|FL043059
EST:     TACGACACCTCCATCATCTTCTTCGACGGCGCCATCGCCCAGATCAACAA                         GCATCTAACTACTTTGGACGATGCTCTGATTCGTACGAAATGGATGAACTG
genomic: TACGACACCTCCATCATCTTCTTCGACGGCGCCATCGCCCAGATCAACAAgtgagcttct ... aaccatacagGCATCTAACTACTTTGGACGATGCTCTGATTCGTACGAAATGGATGAACTG
EST: gi|76934046|gb|DV173701.1|DV173701
EST:     TACGACACCTCCATCATCTTCTTCGACGGCGCCATCGCCCAGATCAACAA                         GCATCTAACTACTTTGGACGATGCTCTGATTCGTACGAAATGGATGAACTG
genomic: TACGACACCTCCATCATCTTCTTCGACGGCGCCATCGCCCAGATCAACAAgtgagcttct ... aaccatacagGCATCTAACTACTTTGGACGATGCTCTGATTCGTACGAAATGGATGAACTG
EST: gi|32827993|gb|CD967671.1|CD967671
EST:     TACGACACCTCCATCATCTTCTTCGACGGCGCCATCGCCCAGATCAACAA                         GCATCTAACTACTTTGGACGATGCTCTGATTCGTACGAAATGGATGAACTG
genomic: TACGACACCTCCATCATCTTCTTCGACGGCGCCATCGCCCAGATCAACAAgtgagcttct ... aaccatacagGCATCTAACTACTTTGGACGATGCTCTGATTCGTACGAAATGGATGAACTG
EST: gi|211073701|gb|FL043065.1|FL043065
EST:     TACGACACCTCCATCATCTTCTTCGACGGCGCCATCGCCCAGATCAACAA                         GCATCTAACTACTTTGGACGATGCTCTGATTCGTACGAAATGGATGAACTG
genomic: TACGACACCTCCATCATCTTCTTCGACGGCGCCATCGCCCAGATCAACAAgtgagcttct ... aaccatacagGCATCTAACTACTTTGGACGATGCTCTGATTCGTACGAAATGGATGAACTG
EST: gi|26455827|gb|CA827410.1|CA827410
EST:     TACGACACCTCCATCATCTTCTTCGACGGCGCCATCGCCCAGATCAACAA                         GCATCTAACTACTTTGGACGATGCTCTGATTCGTACGAAATGGATGAACTG
genomic: TACGACACCTCCATCATCTTCTTCGACGGCGCCATCGCCCAGATCAACAAgtgagcttct ... aaccatacagGCATCTAACTACTTTGGACGATGCTCTGATTCGTACGAAATGGATGAACTG

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: 162

GGCTGCAGGACCACCTCAAGCTCGCGCGGGACTACGCGCTCGAGGGCCTCTACGACACCTCCATCATCTTCTTCGACGGCGCCATCGCCCAGATCAACAAgtgagcttct ... aaccatacagGCATCTAACTACTTTGGACGATGCTCTGATTCGTACGAAATGGATGAACTGCAAGAAAGCAATCTCTGAAGAAGTGGAAATTGTGAAACAGTTGGATGCT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 58

GGCTGCAGGACCACCTCAAGCTCGCGCGGGACTACGCGCTCGAGGGCCTCTACGACACCTCCATCATCTTCTTCGACGGCGCCATCGCCCAGATCAACAAgtgagcttct ... aaccatacagGCATCTAACTACTTTGGACGATGCTCTGATTCGTACGAAATGGATGAACTGCAAGAAAGCAATCTCTGAAGAAGTGGAAATTGTGAAACAGTTGGATGCT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 60

GGCTGCAGGACCACCTCAAGCTCGCGCGGGACTACGCGCTCGAGGGCCTCTACGACACCTCCATCATCTTCTTCGACGGCGCCATCGCCCAGATCAACAAgtgagcttct ... aaccatacagGCATCTAACTACTTTGGACGATGCTCTGATTCGTACGAAATGGATGAACTGCAAGAAAGCAATCTCTGAAGAAGTGGAAATTGTGAAACAGTTGGATGCT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 94

GGCTGCAGGACCACCTCAAGCTCGCGCGGGACTACGCGCTCGAGGGCCTCTACGACACCTCCATCATCTTCTTCGACGGCGCCATCGCCCAGATCAACAAgtgagcttct ... aaccatacagGCATCTAACTACTTTGGACGATGCTCTGATTCGTACGAAATGGATGAACTGCAAGAAAGCAATCTCTGAAGAAGTGGAAATTGTGAAACAGTTGGATGCT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agataatgtcgtttcctcgttttccatgttattaaggttcatcttaaccatacagGCATCTAACTACTTTGGACGATGCTCTGATTCGTACGAAATGGATGAACTGCAAGAAAGCAATCTCTGAAGAAGTGGAAATTGTGAAACAGTTGGATGCT
                                         tcttaac  putative branch site (score: 94)
                         atgttattaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttctttcttattgataaaatatctaggaaagacacttaaaagcctagataatgtcgtttcctcgttttccatgttattaaggttcatcttaaccatacagGCATCTAACTACTTTGGACGATGCTCTGATTCGTACGAAATGGATGAACTGCAAGAAAGCAATCTCTGAAGAAGTGGAAATTGTGAAACAGTTGGATGCT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGTGGA
- - - - - - - - - - - - - -aaagaca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gttcatc