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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtcgacggatgtgcatgcatgctttgccacgcgccttcgttcttccactatgatacagccgccatgacagccccgacggtcatttaacaggattgtaccttgtttttttttttcagATAGAGAGCAACATCGTTAGATGTCCTGATCCAGAGTACGCAGAGAAGATGATAGACGCAATCGACAGAGTACGAGTTCGAGGGGATTCGGTCGGTGGAG

Basic information

species Zea mays
transcript GRMZM2G036861_T01
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G036861_T01 (Zea mays), 3'ss of exon 7
lower sequence: LOC_Os03g14990.1 (Oryza sativa), 3'ss of exon 7
gtcgacggatgtgcatgcatgctttgccacgcgccttcgttcttccactatgatacagccgccatgacagccccgacggtcatttaacaggattgtaccttgtttttttttttcagATAGAGAGCAACATCGTTAGATGTCCTGATCCAGAGTACGCAGAGAAGATGATAGACGCAATCGACAGAGTACGAGTTCGAGGGGATTCGGTCGGTGGAG
                      | ||    |  ||  |  | ||| | | | | ||  | |    ||||| | |    | |||||  | | ||  ||  ||  |||| |||| |||||||| |||||||| |||||||||||||||||||| || ||| |||||||||| || |||||||| | |||||||||| |||| |||||| | ||||| |
---------------------gtctgtg--gttcccaccattttcaagtttaacacttctg----gacagtctctgaaggcatttg-ctgaatattatatttattttattttccagATAGAAAGCAACATTGTTAGATGTCCTGATCCAGAATATGCACAGAAGATGATTGATGCAATCGATAAAGTACGAGTTAGAGGTGATTCGATTGGTGGTG

upper sequence: GRMZM2G036861_T01 (Zea mays), 3'ss of exon 7
lower sequence: GLYMA20G31980.1 (Glycine max), 3'ss of exon 7
gtcgacggatgtgcatgcatgctttgccacgcgccttcgttcttccactatgatacagccgccatgacagccccgacggtcatttaacaggattgtaccttgtttttttttttcagATAGAGAGCAACATCGTTAGATGTCCTGATCCAGAGTACGCAGAGAAGATGATAGACGCAATCGACAGAGTACGAGTTCGAGGGGATTCGGTCGGTGGAG
        || | ||   ||||  ||   |       |    |     ||| |   |      || | |    | |  |   ||       |   |   || |    ||| | ||||| ||||| ||||| ||| ||||||| || || ||||| |||||||||||||||   ||||| ||    || |||||  |||| ||||| || ||||| |
--------atttaca---atgcaatgtttcaaattgactaattattgttataacttatat-tgataatactttctattgatgttctt----accattttttttggaatttatccagATTGAGAGTAACATTGTTCGATGTCCAGACCCGGAGTATGCAGAGAAGATGATATCTGCAATTGATGCTGTGCGAGTGAGAGGTGATTCTGTTGGTGGTG
















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|148950436|gb|EC896004.2|EC896004
EST:     TTGTGCTCCCAGAAGACGCGGTTGATTATGGGTCTGTAACTTTGGAACAG                         ATAGAGAGCAACATCGTTAGATGTCCTGATCCAGAGTACGCAGAGAAGATG
genomic: TTGTGCTCCCAGAAGACGCGGTTGATTATGGGTCTGTAACTTTGGAACAGgtcgacggat ... tttttttcagATAGAGAGCAACATCGTTAGATGTCCTGATCCAGAGTACGCAGAGAAGATG
EST: gi|149096924|gb|EE182722.2|EE182722
EST:     TTGTGCTCCCAGAAGACGCGGTTGATTATGGGTCTGTAACTTTGGAACAG                         ATAGAGAGCAACATCGTTAGATGTCCTGAT
genomic: TTGTGCTCCCAGAAGACGCGGTTGATTATGGGTCTGTAACTTTGGAACAGgtcgacggat ... tttttttcagATAGAGAGCAACATCGTTAGATGTCCTGAT
EST: gi|149088025|gb|EE177228.2|EE177228
EST:     TTGTGCTCCCAGAAGACGCGGTTGATTATGGGTCTGTAACTTTGGAACAG                         ATAGAGAGCAACATCGTTAGATGTCCTGATCCAGAGTACGCAGAGAAGATG
genomic: TTGTGCTCCCAGAAGACGCGGTTGATTATGGGTCTGTAACTTTGGAACAGgtcgacggat ... tttttttcagATAGAGAGCAACATCGTTAGATGTCCTGATCCAGAGTACGCAGAGAAGATG
EST: gi|149089246|gb|EE178450.2|EE178450
EST:     TTGTGCTCCCAGAAGACGCGGTTGATTATGGGTCTGTAACTTTGGAACAG                         ATAGAGAGCAACATCGTTAGATGTCCTGATC
genomic: TTGTGCTCCCAGAAGACGCGGTTGATTATGGGTCTGTAACTTTGGAACAGgtcgacggat ... tttttttcagATAGAGAGCAACATCGTTAGATGTCCTGATC
EST: gi|149106625|gb|EE188518.2|EE188518
EST:     TTGTGCTCCCAGAAGACGCGGTTGATTATGGGTCTGTAACTTTGGAACAG                         ATAGAGAGCAACATCGTTAGATGTCCTGATCCAGAGTA
genomic: TTGTGCTCCCAGAAGACGCGGTTGATTATGGGTCTGTAACTTTGGAACAGgtcgacggat ... tttttttcagATAGAGAGCAACATCGTTAGATGTCCTGATCCAGAGTA
EST: gi|148951094|gb|EC896759.2|EC896759
EST:     TTGTGCTCCCAGAAGACGCGGTTGATTATGGGTCTGTAACTTTGGAACAG                         ATAGAGAGCAACATCGTTAGATGTCCTGATCCAGAGTACGCAGAGAAGATG
genomic: TTGTGCTCCCAGAAGACGCGGTTGATTATGGGTCTGTAACTTTGGAACAGgtcgacggat ... tttttttcagATAGAGAGCAACATCGTTAGATGTCCTGATCCAGAGTACGCAGAGAAGATG
EST: gi|149067437|gb|EE287007.2|EE287007
EST:     TTGTGCTCCCAGAAGACGCGGTTGATTATGGGTCTGTAACTTTGGAACAG                         ATAGAGAGCAACATCGTTAGATGCCCTGA
genomic: TTGTGCTCCCAGAAGACGCGGTTGATTATGGGTCTGTAACTTTGGAACAGgtcgacggat ... tttttttcagATAGAGAGCAACATCGTTAGATGTCCTGA
EST: gi|149098825|gb|EE184838.2|EE184838
EST:     TTGTGCTCCCAGAAGACGCGGTTGATTATGGGTCTGTAACTTTGGAACAG                         ATAGAGAGCAACATCGTTAGATGTCCTGATCCAGAGTACGCAGAGAAGATG
genomic: TTGTGCTCCCAGAAGACGCGGTTGATTATGGGTCTGTAACTTTGGAACAGgtcgacggat ... tttttttcagATAGAGAGCAACATCGTTAGATGTCCTGATCCAGAGTACGCAGAGAAGATG
EST: gi|149071022|gb|EE159425.2|EE159425
EST:     TTGTGCTCCCAGAAGACGCGGTTGATTATGGGTCTGTAACTTTGGAACAG                         ATAGAGAGCAACATCGTT
genomic: TTGTGCTCCCAGAAGACGCGGTTGATTATGGGTCTGTAACTTTGGAACAGgtcgacggat ... tttttttcagATAGAGAGCAACATCGTT

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 3 RNA-Seq libraries.


Block sizes: 47 (upstream exon), 47 (downstream exon)
Score: 23

ATCTTGTCGTTTGTTTCCAAAGTGCATCAGGTTGTGCTCCCAGAAGACGCGGTTGATTATGGGTCTGTAACTTTGGAACAGgtcgacggat ... tttttttcagATAGAGAGCAACATCGTTAGATGTCCTGATCCAGAGTACGCAGAGAAGATGATAGACGCAATCGACAGAGTACGAGTTCGAGGGGATTCGGTCGGTGGAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 526

ATCTTGTCGTTTGTTTCCAAAGTGCATCAGGTTGTGCTCCCAGAAGACGCGGTTGATTATGGGTCTGTAACTTTGGAACAGgtcgacggat ... tttttttcagATAGAGAGCAACATCGTTAGATGTCCTGATCCAGAGTACGCAGAGAAGATGATAGACGCAATCGACAGAGTACGAGTTCGAGGGGATTCGGTCGGTGGAG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 324

ATCTTGTCGTTTGTTTCCAAAGTGCATCAGGTTGTGCTCCCAGAAGACGCGGTTGATTATGGGTCTGTAACTTTGGAACAGgtcgacggat ... tttttttcagATAGAGAGCAACATCGTTAGATGTCCTGATCCAGAGTACGCAGAGAAGATGATAGACGCAATCGACAGAGTACGAGTTCGAGGGGATTCGGTCGGTGGAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ccatgacagccccgacggtcatttaacaggattgtaccttgtttttttttttcagATAGAGAGCAACATCGTTAGATGTCCTGATCCAGAGTACGCAGAGAAGATGATAGACGCAATCGACAGAGTACGAGTTCGAGGGGATTCGGTCGGTGGAG
                    atttaac  putative branch site (score: 324)
                               ttgtaccttgtttttt  putative PPT
                                      ttgtttttttttttca  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtcgacggatgtgcatgcatgctttgccacgcgccttcgttcttccactatgatacagccgccatgacagccccgacggtcatttaacaggattgtaccttgtttttttttttcagATAGAGAGCAACATCGTTAGATGTCCTGATCCAGAGTACGCAGAGAAGATGATAGACGCAATCGACAGAGTACGAGTTCGAGGGGATTCGGTCGGTGGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GTGGAG