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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttagttgattttcactacagctgtttgcttttaatcgagcatattaattcaatgcctactttctttattccctgaactgtagGTTTCTGTTGAACTATCATTCATGGAAGCTGTCCAAGGTTGCAGAAAAACCATTACGTACGAAGCTGATACTTTTTGTGGAACTTGCA

Basic information

species Zea mays
transcript GRMZM2G118316_T01
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G118316_T01 (Zea mays), 3'ss of exon 8
lower sequence: LOC_Os12g07060.1 (Oryza sativa), 3'ss of exon 8
-gttagttgattttcactacagctgtttgcttt-taatcgagcat-attaattcaatgcctacttt-----ctttattccctgaactgtagGTTTCTGTTGAACTATCATTCATGGAAGCTGTCCAAGGTTGCAGAAAAACCATTACGTACGAAGCTGATACTTTTTGTGGAACTTGCA
  |   ||| | |||| || |    |||| ||  | |   || ||   | |||  | || ||||||     |||| || ||  || | |||||| |  |  ||||||||||||||||||| |||||||| ||||||||||| ||| | || || ||||||  ||| || |  |||||||
gttctattgttgttcatta-aatgatttgtttaatgacaaagaattgattattggaagcttacttttttctctttttttccccaaatatagGTTCCAATCAAACTATCATTCATGGAAGCCGTCCAAGGCTGCAGAAAAACTATTGCATATGAGGCTGATGTTTTCTGCGATACTTGCA

upper sequence: GRMZM2G118316_T01 (Zea mays), 3'ss of exon 8
lower sequence: Vv13s0064g01360.t01 (Vitis vinifera), 3'ss of exon 8
------gttagttgattttcactacagctgtttgcttttaatcgagcatattaattcaatgcctactttctttattccctgaactgtagGTTTCTGTTGAACTATCATTCATGGAAGCTGTCCAAGGTTGCAGAAAAACCATTACGTACGAAGCTGATACTTTTTGTGGAACTTGCA
      ||      || ||   |   | | | |  || |  |  ||  |   |     |    | | || |||||||     |   ||||||||  |||||||||| ||||||||||||||||| || ||||  |||||  | || |   || ||| |     ||||| | ||||  
gtttctgtcctcccatattttttcatgatttctttttgtgcttcagagttacatcattaacatttcattttttattcatc--atgatagGTTTCCATTGAACTATCTTTCATGGAAGCTGTCCAGGGATGCACTAAAACTGTAACATTTCAAACTGCTTTGCCTTGTGAAGCTTGTG
















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|76922542|gb|DV169052.1|DV169052
EST:     ATCTTTGATAATGCATACAGAGGTGGCCAAGATGTCAAG                         GTTTCTGTTGAACTATCATTCATGGAAGCTGTCCAAGGTTGCAGAAAAACC
genomic: ATCTTTGATAATGCATACAGAGGTGGCCAAGATGTCAAGgttagttgat ... tgaactgtagGTTTCTGTTGAACTATCATTCATGGAAGCTGTCCAAGGTTGCAGAAAAACC
EST: gi|149101262|gb|EE187374.2|EE187374
EST:     ATCTTTGATAATGCATACAGAGGTGGCCAAGATGTCAAG                         GTTTCTGTTGAACTATCATTCATGGAAGCTGTCCAAGGTTGCAGAAAAACC
genomic: ATCTTTGATAATGCATACAGAGGTGGCCAAGATGTCAAGgttagttgat ... tgaactgtagGTTTCTGTTGAACTATCATTCATGGAAGCTGTCCAAGGTTGCAGAAAAACC
EST: gi|78088193|gb|DV516586.1|DV516586
EST:     ATCTTTGATAATGCATACAGAGGTGGCCAAGATGTCAAG                         GTTTCTGTTGAACTATCATTCATGGAAGCTGTCCAAGGTTGCAGAAAAACC
genomic: ATCTTTGATAATGCATACAGAGGTGGCCAAGATGTCAAGgttagttgat ... tgaactgtagGTTTCTGTTGAACTATCATTCATGGAAGCTGTCCAAGGTTGCAGAAAAACC
EST: gi|93017256|gb|EB642776.1|EB642776
EST:     ATCTTTGATAATGCATACAGAGGTGGCCAAGATGTCAAG                         GTTTCTGTTGAACTATCATTCATGGAAGCTGTCCAAGGTTGCAGAAAAACC
genomic: ATCTTTGATAATGCATACAGAGGTGGCCAAGATGTCAAGgttagttgat ... tgaactgtagGTTTCTGTTGAACTATCATTCATGGAAGCTGTCCAAGGTTGCAGAAAAACC
EST: gi|71757145|gb|DR955082.1|DR955082
EST:     ATCTTTGATAATGCATACAGAGGTGGCCAAGATGTCAAG                         GTTTCTGCTGAACTATCATTCATGGAAGCTGTCCAAGGTTGCAGAAAAACC
genomic: ATCTTTGATAATGCATACAGAGGTGGCCAAGATGTCAAGgttagttgat ... tgaactgtagGTTTCTGTTGAACTATCATTCATGGAAGCTGTCCAAGGTTGCAGAAAAACC
EST: gi|71771526|gb|DR969463.1|DR969463
EST:     ATCTTTGATAATGCATACAGAGGTGGCCAAGATGTCAAG                         GTTTCTGTTGAACTATCATTCATGGAAGCTGTCCAAGGTTGCAGAAAAACC
genomic: ATCTTTGATAATGCATACAGAGGTGGCCAAGATGTCAAGgttagttgat ... tgaactgtagGTTTCTGTTGAACTATCATTCATGGAAGCTGTCCAAGGTTGCAGAAAAACC
EST: gi|71427931|gb|DR808981.1|DR808981
EST:     ATCTTTGATAATGCATACAGAGGTGGCCAAGATGTCAAG                         GTTTCTGTTGAACTATCATTCATGGAAGCTGTCCAAGGTTGCAGAAAAACC
genomic: ATCTTTGATAATGCATACAGAGGTGGCCAAGATGTCAAGgttagttgat ... tgaactgtagGTTTCTGTTGAACTATCATTCATGGAAGCTGTCCAAGGTTGCAGAAAAACC
EST: gi|91049687|gb|EB160105.1|EB160105
EST:     ATCTTTGATAATGCATACAGAGGTGGCCAAGATGTCAAG                         GTTTCTGTTGAACTATCATTCATGGAAGCTGTCCAAGGTTGCAGAAAAACC
genomic: ATCTTTGATAATGCATACAGAGGTGGCCAAGATGTCAAGgttagttgat ... tgaactgtagGTTTCTGTTGAACTATCATTCATGGAAGCTGTCCAAGGTTGCAGAAAAACC
EST: gi|34391167|gb|CF384395.1|CF384395
EST:     ATCTTTGATAATGCATACAGAGGTGGCCAAGATGTTAAG                         GTTTCTGTTGAACTATCATTCATGGAAGCTGTCCAAGGTTGCAGAAAAACC
genomic: ATCTTTGATAATGCATACAGAGGTGGCCAAGATGTCAAGgttagttgat ... tgaactgtagGTTTCTGTTGAACTATCATTCATGGAAGCTGTCCAAGGTTGCAGAAAAACC
EST: gi|211533908|gb|FL308317.1|FL308317
EST:     ATCTTTGATAATGCATACAGAGGTGGCCAAGATGTTAAG                         GTTTCTGTTGAACTATCATTCATGGAAGCTGTCCAAGGTTGCAGAAAAACC
genomic: ATCTTTGATAATGCATACAGAGGTGGCCAAGATGTCAAGgttagttgat ... tgaactgtagGTTTCTGTTGAACTATCATTCATGGAAGCTGTCCAAGGTTGCAGAAAAACC
EST: gi|91049823|gb|EB160241.1|EB160241
EST:     ATCTTTGATAATGCATACAGAGGTGGCCAAGATGTCAAG                         GTTTCTGTTGAACTATCATTCATGGAAGCTGTCCAAGGTTGCAGAAAAACC
genomic: ATCTTTGATAATGCATACAGAGGTGGCCAAGATGTCAAGgttagttgat ... tgaactgtagGTTTCTGTTGAACTATCATTCATGGAAGCTGTCCAAGGTTGCAGAAAAACC
EST: gi|71769072|gb|DR967009.1|DR967009
EST:     ATCTTTGATAATGCATACAGAGGTGGCCAAGATGTCAAG                         GTTTCTGTTGAACTATCATTCATGGAAGCTGTCCAAGGTTGCAGAAAAACC
genomic: ATCTTTGATAATGCATACAGAGGTGGCCAAGATGTCAAGgttagttgat ... tgaactgtagGTTTCTGTTGAACTATCATTCATGGAAGCTGTCCAAGGTTGCAGAAAAACC

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: 39 (upstream exon), 49 (downstream exon)
Score: 110

ATCTTTGATAATGCATACAGAGGTGGCCAAGATGTCAAGgttagttgat ... tgaactgtagGTTTCTGTTGAACTATCATTCATGGAAGCTGTCCAAGGTTGCAGAAAAACCATTACGTACGAAGCTGATACTTTTTGTGGAACTTGCA


Block sizes: 44 (upstream exon), 49 (downstream exon)
Score: 129

ATCTTTGATAATGCATACAGAGGTGGCCAAGATGTCAAGgttagttgat ... tgaactgtagGTTTCTGTTGAACTATCATTCATGGAAGCTGTCCAAGGTTGCAGAAAAACCATTACGTACGAAGCTGATACTTTTTGTGGAACTTGCA


Block sizes: 39 (upstream exon), 49 (downstream exon)
Score: 159

ATCTTTGATAATGCATACAGAGGTGGCCAAGATGTCAAGgttagttgat ... tgaactgtagGTTTCTGTTGAACTATCATTCATGGAAGCTGTCCAAGGTTGCAGAAAAACCATTACGTACGAAGCTGATACTTTTTGTGGAACTTGCA


Block sizes: 39 (upstream exon), 49 (downstream exon)
Score: 154

ATCTTTGATAATGCATACAGAGGTGGCCAAGATGTCAAGgttagttgat ... tgaactgtagGTTTCTGTTGAACTATCATTCATGGAAGCTGTCCAAGGTTGCAGAAAAACCATTACGTACGAAGCTGATACTTTTTGTGGAACTTGCA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cttttaatcgagcatattaattcaatgcctactttctttattccctgaactgtagGTTTCTGTTGAACTATCATTCATGGAAGCTGTCCAAGGTTGCAGAAAAACCATTACGTACGAAGCTGATACTTTTTGTGGAACTTGCA
              tattaat  putative branch site (score: 154)
                         tgcctactttctttat  putative PPT
             atattaattcaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttagttgattttcactacagctgtttgcttttaatcgagcatattaattcaatgcctactttctttattccctgaactgtagGTTTCTGTTGAACTATCATTCATGGAAGCTGTCCAAGGTTGCAGAAAAACCATTACGTACGAAGCTGATACTTTTTGTGGAACTTGCA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT