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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aagggcaactggtctgaaacatatcatattcatatccttttgttcatttttcttttacaattccttgcatatcaagcaaataattgttttaatattatagGGAGAGGGTTAGGCAACGATTGGCTTTGTACCAAGGTGTATGTCCGGTTCAAATGGAATTTTCTGATGATGCTGAGAAGACATTTGGCAATGCTTTGTCT

Basic information

species Zea mays
transcript GRMZM2G152686_T01
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G152686_T01 (Zea mays), 3'ss of exon 10
lower sequence: LOC_Os01g47080.1 (Oryza sativa), 3'ss of exon 10
aagggcaactggtctgaaacatatcatattcatatccttttgttcatttttcttttacaattccttgcatatcaagcaaataatt-gttttaata------ttatagGGAGAGGGTTAGGCAACGATTGGCTTTGTACCAAGGTGTATGTCCGGTTCAAATGGAATTTTCTGATGATGCTGAGAAGACATTTGGCAATGCTTTGTCT
|| |        ||| |||  ||| || ||      || ||||||||||||| |||| |||    |   | |||||||  ||||| || || ||       || ||||||||| ||||| |||||||||||||||||||||||||||||||| || || |||||||||||||||||||||||||||||||||||  | |||||||| 
aatgtttggctctctaaaa-gtatgatgttt-----ctcttgttcatttttcctttataatatggtatct-tcaagcacctaattagtgttgatggtatgtttgtagGGAGAGAGTTAGACAACGATTGGCTTTGTACCAAGGTGTATGTCCAGTCCAGATGGAATTTTCTGATGATGCTGAGAAGACATTTGGTGACGCTTTGTCA
















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|60401124|gb|DN233931.1|DN233931
EST:     ATCTGGCACTATTTTTGCCTTCACAGACGA                         GGAGAGAGTTAGGCAACGATTGGCTTTGTACCAAGGTGTATGTCCGGTTCA
genomic: ATCTGGCACTATTTTTGCCTTTACAGATGAgtaagttttc ... aatattatagGGAGAGGGTTAGGCAACGATTGGCTTTGTACCAAGGTGTATGTCCGGTTCA
EST: gi|78023476|gb|DV491863.1|DV491863
EST:     CTGCTTAGTCACTACCGTCCATCTGGCACTATTTTTGCCTTCACAGACGA                         GGAGAGAGTTAGGCAACGATTGGCTTTGTACCAAGGTGTATGTCCGGTTCA
genomic: CTGCTTAGTCACTACCGTCCATCTGGCACTATTTTTGCCTTTACAGATGAgtaagttttc ... aatattatagGGAGAGGGTTAGGCAACGATTGGCTTTGTACCAAGGTGTATGTCCGGTTCA
EST: gi|60346042|gb|DN213015.1|DN213015
EST:     CTGCTTAGTCACTACCGTCCATCTGGCACTATTTTTGCCTTTACAGATGA                         GGAGAGGGTTAGGCAACGATTGGCTTTGTACCAAGGTGTATGTCCGGTTCA
genomic: CTGCTTAGTCACTACCGTCCATCTGGCACTATTTTTGCCTTTACAGATGAgtaagttttc ... aatattatagGGAGAGGGTTAGGCAACGATTGGCTTTGTACCAAGGTGTATGTCCGGTTCA
EST: gi|5499208|gb|AI855075.1|AI855075
EST:     CTGCTTAGTCACTACCGTCCATCTGGCACTATTTTTGCCTTCACAGACGA                         GGAGAGAGTTAGGCAACGATTGGCTTTGTACCAAGGTGTATGTCCGGTTCA
genomic: CTGCTTAGTCACTACCGTCCATCTGGCACTATTTTTGCCTTTACAGATGAgtaagttttc ... aatattatagGGAGAGGGTTAGGCAACGATTGGCTTTGTACCAAGGTGTATGTCCGGTTCA
EST: gi|5686894|gb|AI939808.1|AI939808
EST:     TTTTGCCTTCACAGACGA                         GGAGAGAGTTAGGCAACGATTGGCTTTGTACCAAGGTGTATGTCCGGTTCA
genomic: TTTTGCCTTTACAGATGAgtaagttttc ... aatattatagGGAGAGGGTTAGGCAACGATTGGCTTTGTACCAAGGTGTATGTCCGGTTCA
EST: gi|211222802|gb|FL455247.1|FL455247
EST:     CTGCTTAGTCACTACCGTCCATCTGGCACTATTTTTGCCTTTACAGATGA                         GGAGAGGGTTAGGCAACGATTGGCTTTGTACCAAGGTGTATGTCCGGTTCA
genomic: CTGCTTAGTCACTACCGTCCATCTGGCACTATTTTTGCCTTTACAGATGAgtaagttttc ... aatattatagGGAGAGGGTTAGGCAACGATTGGCTTTGTACCAAGGTGTATGTCCGGTTCA
EST: gi|60359110|gb|DN226083.1|DN226083
EST:     CTGCTTAGTCACTACCGTCCATCTGGCACTATTTTTGCCTTTACAGATGA                         GGAGAGGGTTAGGCAACGATTGGCTTTGTACCAAGGTGTATGTCCGGTTCA
genomic: CTGCTTAGTCACTACCGTCCATCTGGCACTATTTTTGCCTTTACAGATGAgtaagttttc ... aatattatagGGAGAGGGTTAGGCAACGATTGGCTTTGTACCAAGGTGTATGTCCGGTTCA
EST: gi|211222803|gb|FL455248.1|FL455248
EST:     TATTTTTGCCTTTACAGATGA                         GGAGAGGGTTAGGCAACGATTGGCTTTGTACCAAGGTGTATGTCCGGTTCA
genomic: TATTTTTGCCTTTACAGATGAgtaagttttc ... aatattatagGGAGAGGGTTAGGCAACGATTGGCTTTGTACCAAGGTGTATGTCCGGTTCA
EST: gi|213173762|gb|FM184221.1|FM184221
EST:     CTCCTTAGTCACTACCGTCCATCTGGCACTATTTTTGCCTTCACAGATGA                         GGAGAGAGTTAGGCAACGATTGGCTTTGTACCAAGGTGTATGTCCGGTTCA
genomic: CTGCTTAGTCACTACCGTCCATCTGGCACTATTTTTGCCTTTACAGATGAgtaagttttc ... aatattatagGGAGAGGGTTAGGCAACGATTGGCTTTGTACCAAGGTGTATGTCCGGTTCA
EST: gi|148934385|gb|EC878415.2|EC878415
EST:     CTGCTTAGTCACTACCGTCCATCTGGCACTATTTTTGCCTTTACAGATGA                         GGAGAGGGTTAGGCAACGATTGGCTTTGTACCAAGGTGTATGTCCGGTTCA
genomic: CTGCTTAGTCACTACCGTCCATCTGGCACTATTTTTGCCTTTACAGATGAgtaagttttc ... aatattatagGGAGAGGGTTAGGCAACGATTGGCTTTGTACCAAGGTGTATGTCCGGTTCA
EST: gi|6020916|gb|AW065844.1|AW065844
EST:     CTGCTTAGTCACTACCGTCCATCTGGCACTATTTTTGCCTTCACAGACGA                         GGAGAGAGTTAGGCAACGATTGGCTTTGTACCAAGGTGTATGTCCGGTTCA
genomic: CTGCTTAGTCACTACCGTCCATCTGGCACTATTTTTGCCTTTACAGATGAgtaagttttc ... aatattatagGGAGAGGGTTAGGCAACGATTGGCTTTGTACCAAGGTGTATGTCCGGTTCA
EST: gi|78125189|gb|DV543573.1|DV543573
EST:     CTGCTTAGTCACTACCGTCCATCTGGCACTATTTTTGCCTTTACAGATGA                         GGAGAGGGTTAGGCAACGATTGGCTTTGTACCAAGGTGTATGTCCGGTTCA
genomic: CTGCTTAGTCACTACCGTCCATCTGGCACTATTTTTGCCTTTACAGATGAgtaagttttc ... aatattatagGGAGAGGGTTAGGCAACGATTGGCTTTGTACCAAGGTGTATGTCCGGTTCA
EST: gi|21843365|gb|BQ703946.1|BQ703946
EST:     CTGCTTAGTCACTACCGTCCATCTGGCACTATTTTTGCCTTCACAGACGA                         GGAGAGAGTTAGGCAACGATTGGCTTTGTACCAAGGTGTATGTCCGGTTCA
genomic: CTGCTTAGTCACTACCGTCCATCTGGCACTATTTTTGCCTTTACAGATGAgtaagttttc ... aatattatagGGAGAGGGTTAGGCAACGATTGGCTTTGTACCAAGGTGTATGTCCGGTTCA
EST: gi|14204276|gb|BG837953.1|BG837953
EST:     CTGCTTAGTCACTACCGTCCATCTGGCACTATTTTTGCCTTTACAGATGA                         GGAGAGGGTTAGGCAACGATTGGCTTTGTACCAAGGTGTATGTCCGGTTCA
genomic: CTGCTTAGTCACTACCGTCCATCTGGCACTATTTTTGCCTTTACAGATGAgtaagttttc ... aatattatagGGAGAGGGTTAGGCAACGATTGGCTTTGTACCAAGGTGTATGTCCGGTTCA
EST: gi|211384112|gb|FL133262.1|FL133262
EST:     CTGCTTAGTCACTACCGTCCATCTGGCACTATTTTTGCCTTCACAAACGA                         GGAGAGAGTTAG
genomic: CTGCTTAGTCACTACCGTCCATCTGGCACTATTTTTGCCTTTACAGATGAgtaagttttc ... aatattatagGGAGAGGGTTAG

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), 48 (downstream exon)
Score: 192

CCCTTCGAACATCAATAGTGGTTTTCACTAGGACGGGATTTATGGCTATACTGCTTAGTCACTACCGTCCATCTGGCACTATTTTTGCCTTTACAGATGAgtaagttttc ... aatattatagGGAGAGGGTTAGGCAACGATTGGCTTTGTACCAAGGTGTATGTCCGGTTCAAATGGAATTTTCTGATGATGCTGAGAAGACATTTGGCAATGCTTTGTCT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 104

CCCTTCGAACATCAATAGTGGTTTTCACTAGGACGGGATTTATGGCTATACTGCTTAGTCACTACCGTCCATCTGGCACTATTTTTGCCTTTACAGATGAgtaagttttc ... aatattatagGGAGAGGGTTAGGCAACGATTGGCTTTGTACCAAGGTGTATGTCCGGTTCAAATGGAATTTTCTGATGATGCTGAGAAGACATTTGGCAATGCTTTGTCT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 99

CCCTTCGAACATCAATAGTGGTTTTCACTAGGACGGGATTTATGGCTATACTGCTTAGTCACTACCGTCCATCTGGCACTATTTTTGCCTTTACAGATGAgtaagttttc ... aatattatagGGAGAGGGTTAGGCAACGATTGGCTTTGTACCAAGGTGTATGTCCGGTTCAAATGGAATTTTCTGATGATGCTGAGAAGACATTTGGCAATGCTTTGTCT


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 225

CCCTTCGAACATCAATAGTGGTTTTCACTAGGACGGGATTTATGGCTATACTGCTTAGTCACTACCGTCCATCTGGCACTATTTTTGCCTTTACAGATGAgtaagttttc ... aatattatagGGAGAGGGTTAGGCAACGATTGGCTTTGTACCAAGGTGTATGTCCGGTTCAAATGGAATTTTCTGATGATGCTGAGAAGACATTTGGCAATGCTTTGTCT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atttttcttttacaattccttgcatatcaagcaaataattgttttaatattatagGGAGAGGGTTAGGCAACGATTGGCTTTGTACCAAGGTGTATGTCCGGTTCAAATGGAATTTTCTGATGATGCTGAGAAGACATTTGGCAATGCTTTGTCT
                                         ttttaat  putative branch site (score: 225)
                       atatcaagcaaataat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aagggcaactggtctgaaacatatcatattcatatccttttgttcatttttcttttacaattccttgcatatcaagcaaataattgttttaatattatagGGAGAGGGTTAGGCAACGATTGGCTTTGTACCAAGGTGTATGTCCGGTTCAAATGGAATTTTCTGATGATGCTGAGAAGACATTTGGCAATGCTTTGTCT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - gcaactg
- - - - - - - - aaacata
- - - - - - - - - - - - - - ttcatat
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tccttgc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - caagcaa