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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaatttgcatcaagttatcttgccatgcagtcacagtggcaaggactattgcatgtctgatcgcaatcctgtcatgcccatttgtgctaatctgcaccgtacatcatagcttcagaagtttgctaatttatctttctttgtgaatgaaaaatggtcaacagAGTCTTGTATTTGCAAGTGGAGAAGAGAGGTCCCGGAGGGAAGAAATCAAGCTGCAAGATATCCAAAGGAGATGGGTTGCATCTAACCGATGGGCTGAAG

Basic information

species Zea mays
transcript GRMZM2G084181_T01
intron # 26
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G084181_T01 (Zea mays), 3'ss of exon 26
lower sequence: LOC_Os04g52900.2 (Oryza sativa), 3'ss of exon 26
---------------------gtaatttgcatcaagttatcttgccatgcagtcacagt-ggcaaggactattgcatgtctgatcgcaatcc-tgtcatgcccatttgtgctaatctgcaccgt-acatcatagc-------ttcagaagtttgctaatttatctttctttgtgaatgaaaaatggtcaacagAGTCTTGTATTTGCAAGTGGAGAAGAGAGGTCCCGGAGGGAAGAAATCAAGCTGCAAGATATCCAAAGGAGATGGGTTGCATCTAACCGATGGGCTGAAG
                     ||  ||   ||     ||      |||  |    |  | |  ||  | || ||  ||        |||||| ||| |  | |  | |  | | | | ||| ||    |   |||       || | | || | || ||| | |||| ||| ||| ||||   |  |  ||||| |||||||||||    ||| || |||||||  || | |||||||| |||| ||||||||||||| ||||  ||||| |||||||||||||||||||  |
gtgtttttctatcatctcgatgttcttgaaatttgtgtactacagcataaaacagcgtttgataaataataatgagtgatgctgttcaatccatgttacactccatcgctcaagttttcacagttggctttcagcgaaattattgatatgtgttctgattcaacttttttt-tgactgaa---ttattgacagACTCTTGTATTTGGGGATGGTGAGGAGAGGTTGCGAAAGGAAGAAAGCAAGATGCAAGATATCCAGAGGAAGTGGGTAGCATCTAACCGATGGGCTGTTG
















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|32836693|gb|CD976371.1|CD976371
EST:     ACAGGACCTAGCAACGCAGAATACCTCAAG                         AGTCTTGTATATGGAAGTGGAGAAGAGAGGTCCCGGAGGGAAGAAATCAAG
genomic: ACAGGACCTAGCAACGCAGAATACCTCAAGgtaatttgca ... tggtcaacagAGTCTTGTATTTGCAAGTGGAGAAGAGAGGTCCCGGAGGGAAGAAATCAAG
EST: gi|32837560|gb|CD977238.1|CD977238
EST:     ACAGGACCTAGCAACGCAGAATACCTCAAG                         AGTCTTGTATATGGAAGTGGAGAAGAGAGGTCCCGGAGGGAAGAAATCAAG
genomic: ACAGGACCTAGCAACGCAGAATACCTCAAGgtaatttgca ... tggtcaacagAGTCTTGTATTTGCAAGTGGAGAAGAGAGGTCCCGGAGGGAAGAAATCAAG
EST: gi|71768567|gb|DR966504.1|DR966504
EST:     TCTCCAAGATGGTGCAAAGTACAGGACCTAGCAACGCAGAATACCTCAAG                         AGTCTTGTATTTGCAAGTGGAGAAGAGAGGTCCCGGAGGGAAGAAATCAAG
genomic: TCTCCAAGATGGTGCAAAGTACAGGACCTAGCAACGCAGAATACCTCAAGgtaatttgca ... tggtcaacagAGTCTTGTATTTGCAAGTGGAGAAGAGAGGTCCCGGAGGGAAGAAATCAAG
EST: gi|71768566|gb|DR966503.1|DR966503
EST:     CTAGCAACGCAGAATACCTCAAG                         AGTCTTGTATTTGCAAGTGGAGAAGAGAGGTCCCGGAGGGAAGAAATCAAG
genomic: CTAGCAACGCAGAATACCTCAAGgtaatttgca ... tggtcaacagAGTCTTGTATTTGCAAGTGGAGAAGAGAGGTCCCGGAGGGAAGAAATCAAG
EST: gi|32836886|gb|CD976564.1|CD976564
EST:     GTACAGGACCTAGCAACGCAGAATACCTCAAG                         AGTCTTGTATATGGAAGTGGAGAAGAGAGGTCCCGGAGGGAAGAAATCAAG
genomic: GTACAGGACCTAGCAACGCAGAATACCTCAAGgtaatttgca ... tggtcaacagAGTCTTGTATTTGCAAGTGGAGAAGAGAGGTCCCGGAGGGAAGAAATCAAG
EST: gi|32931235|gb|CF036047.1|CF036047
EST:     CAGGACCTAGCAACGCAGAATACCTCAAG                         AGTCTTGTATATGGAGGTGGAGAAGAGAGGTCCCGGAGGGAAGAAATCAAG
genomic: CAGGACCTAGCAACGCAGAATACCTCAAGgtaatttgca ... tggtcaacagAGTCTTGTATTTGCAAGTGGAGAAGAGAGGTCCCGGAGGGAAGAAATCAAG

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: 247

TCTGGAATTCGACTCTCCTGAGAATCTTCTAAGCAACGAGGGGAGTGCTTTCTCCAAGATGGTGCAAAGTACAGGACCTAGCAACGCAGAATACCTCAAGgtaatttgca ... tggtcaacagAGTCTTGTATTTGCAAGTGGAGAAGAGAGGTCCCGGAGGGAAGAAATCAAGCTGCAAGATATCCAAAGGAGATGGGTTGCATCTAACCGATGGGCTGAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 466

TCTGGAATTCGACTCTCCTGAGAATCTTCTAAGCAACGAGGGGAGTGCTTTCTCCAAGATGGTGCAAAGTACAGGACCTAGCAACGCAGAATACCTCAAGgtaatttgca ... tggtcaacagAGTCTTGTATTTGCAAGTGGAGAAGAGAGGTCCCGGAGGGAAGAAATCAAGCTGCAAGATATCCAAAGGAGATGGGTTGCATCTAACCGATGGGCTGAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 1056

TCTGGAATTCGACTCTCCTGAGAATCTTCTAAGCAACGAGGGGAGTGCTTTCTCCAAGATGGTGCAAAGTACAGGACCTAGCAACGCAGAATACCTCAAGgtaatttgca ... tggtcaacagAGTCTTGTATTTGCAAGTGGAGAAGAGAGGTCCCGGAGGGAAGAAATCAAGCTGCAAGATATCCAAAGGAGATGGGTTGCATCTAACCGATGGGCTGAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 216

TCTGGAATTCGACTCTCCTGAGAATCTTCTAAGCAACGAGGGGAGTGCTTTCTCCAAGATGGTGCAAAGTACAGGACCTAGCAACGCAGAATACCTCAAGgtaatttgca ... tggtcaacagAGTCTTGTATTTGCAAGTGGAGAAGAGAGGTCCCGGAGGGAAGAAATCAAGCTGCAAGATATCCAAAGGAGATGGGTTGCATCTAACCGATGGGCTGAAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tagcttcagaagtttgctaatttatctttctttgtgaatgaaaaatggtcaacagAGTCTTGTATTTGCAAGTGGAGAAGAGAGGTCCCGGAGGGAAGAAATCAAGCTGCAAGATATCCAAAGGAGATGGGTTGCATCTAACCGATGGGCTGAAG
              tgctaat  putative branch site (score: 216)
                 taatttatctttcttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaatttgcatcaagttatcttgccatgcagtcacagtggcaaggactattgcatgtctgatcgcaatcctgtcatgcccatttgtgctaatctgcaccgtacatcatagcttcagaagtttgctaatttatctttctttgtgaatgaaaaatggtcaacagAGTCTTGTATTTGCAAGTGGAGAAGAGAGGTCCCGGAGGGAAGAAATCAAGCTGCAAGATATCCAAAGGAGATGGGTTGCATCTAACCGATGGGCTGAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG