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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AGTTTTTGCAAGACTTGCAAAGGAGAACAGGTAGTGAAGGGGAAAACGTCAGTCAAGCTAGATATAGCCGCAGgtaaggaggaattttctttactgatatatgtgtatgcttgacatgaactccatcccaaattataggttcttttggattttctaggtacatagcttgcacc...

Basic information

species Zea mays
transcript GRMZM2G118316_T01
intron # 12
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G118316_T01 (Zea mays), 5'ss of exon 12
lower sequence: LOC_Os12g07060.1 (Oryza sativa), 5'ss of exon 12
AGTTTTTGCAAGACTTGCAAAGGAGAACAGGTAGTGAAGGGGAAAACGTCAGTCAAGCTAGATATAGCCGCAGgtaaggaggaattttctttactgatatatgtgtatgcttgacatgaactccatcccaaattataggttcttttggattttctaggtacatagcttgcacc
| |||||||||||| ||||| || |||||| |||||||||||||||  ||||||||||| || |||   || |||||| |  | |    | |||  || ||| |||||| ||||||||     | | ||   | ||     | |     || |  |  | | |   | ||  |
AATTTTTGCAAGACATGCAAGGGTGAACAGCTAGTGAAGGGGAAAAAATCAGTCAAGCTCGACATAATGGCTGgtaagaaaaattcaagtataccaatttatctgtatgattgacatgtgaatcctgccttgtaattataacgtgaaatttatgcatatgcttgtttggcttc
















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|149101261|gb|EE187373.2|EE187373
EST:     AGAACAGGTAGTGAAGGGGAAAACGTCAGTCAAGCTAGATATAGCCGCAG                         GAAGTGACGATAATGACATCATGAAGGTTTTTGGTAAGGGTGGTGCAGATG
genomic: AGAACAGGTAGTGAAGGGGAAAACGTCAGTCAAGCTAGATATAGCCGCAGgtaaggagga ... ttttcttcagGAAGTGACGATAATGACATCATGAAGGTTTTTGGTAAGGGTGGTGCAGATG
EST: gi|60397506|gb|DN230322.1|DN230322
EST:     AGAACAGGTAGTGAAGGGGAAAACGTCAGTCAAGCTAGATATAGCCGCAG                         GAAGTGACGATAATGACATCATGAAGGTTTTTGGTAAGGGTGGTGCAGATG
genomic: AGAACAGGTAGTGAAGGGGAAAACGTCAGTCAAGCTAGATATAGCCGCAGgtaaggagga ... ttttcttcagGAAGTGACGATAATGACATCATGAAGGTTTTTGGTAAGGGTGGTGCAGATG
EST: gi|93017255|gb|EB642775.1|EB642775
EST:     AAAACGTCAGTCAAGCTAGATATAGCCGCAG                         GAAGTGACGATAATGACATCATGAAGGTTTTTGGTAAGGGTGGTGCAGATG
genomic: AAAACGTCAGTCAAGCTAGATATAGCCGCAGgtaaggagga ... ttttcttcagGAAGTGACGATAATGACATCATGAAGGTTTTTGGTAAGGGTGGTGCAGATG
EST: gi|211267316|gb|FL091730.1|FL091730
EST:     AGAACAGGTAGTGAAGGGGAAAACGTCAGTCAAGCTAGATATAGCCGCAG                         GAAGTGACGATAATGACATCATGAAGGTTTTTGGTAAGGGTGGTGCAGATG
genomic: AGAACAGGTAGTGAAGGGGAAAACGTCAGTCAAGCTAGATATAGCCGCAGgtaaggagga ... ttttcttcagGAAGTGACGATAATGACATCATGAAGGTTTTTGGTAAGGGTGGTGCAGATG
EST: gi|17929416|gb|BM266376.1|BM266376
EST:     AGAACAGGTAGTGAAGGGGAAAACGTCAGTCAAGCTAGATATAGCCGC--                         --AGTGACGATAATGACATCATGAAGGTTTTTGGTAAGGGTGGTGCAGATG
genomic: AGAACAGGTAGTGAAGGGGAAAACGTCAGTCAAGCTAGATATAGCCGCAGgtaaggagga ... ttttcttcagGAAGTGACGATAATGACATCATGAAGGTTTTTGGTAAGGGTGGTGCAGATG
EST: gi|86469547|gb|DY235917.1|DY235917
EST:     AGAACAGGTAGTGAAGGGGAAAACGTCAGTCAAGCTAGATATAGCCGCAG                         GAAGTGACGATAATGACATCATGAAGGTTTTTGGTAAGGGTGGTGCAGATG
genomic: AGAACAGGTAGTGAAGGGGAAAACGTCAGTCAAGCTAGATATAGCCGCAGgtaaggagga ... ttttcttcagGAAGTGACGATAATGACATCATGAAGGTTTTTGGTAAGGGTGGTGCAGATG
EST: gi|60398827|gb|DN231643.1|DN231643
EST:     AGAACAGGTAGTGAAGGGGAAAACGTCAGTCAAGCTAGATATAGCCGCAG                         GAAGTGACGATAATGACATCATGAAGGTTTTTGGTAAGGGTGGTGCAGATG
genomic: AGAACAGGTAGTGAAGGGGAAAACGTCAGTCAAGCTAGATATAGCCGCAGgtaaggagga ... ttttcttcagGAAGTGACGATAATGACATCATGAAGGTTTTTGGTAAGGGTGGTGCAGATG
EST: gi|211267317|gb|FL091731.1|FL091731
EST:     AGAACAGGTAGTGAAGGGGAAAACGTCAGTCAAGCTAGATATAGCCGCAG                         GAAGTGACGATAATGACATCATGAAGGTTTTTGGTAAGGGTGGTGCAGATG
genomic: AGAACAGGTAGTGAAGGGGAAAACGTCAGTCAAGCTAGATATAGCCGCAGgtaaggagga ... ttttcttcagGAAGTGACGATAATGACATCATGAAGGTTTTTGGTAAGGGTGGTGCAGATG
EST: gi|34391167|gb|CF384395.1|CF384395
EST:     AGAACAGGTAGTGAAGGGGAAAACGTCAGTCAAGCTAGACATAGCCGCAG                         GAAGTGACGATAATGACATCATGAAGGTTTTTGGTAAGGGTGGTGCAGATG
genomic: AGAACAGGTAGTGAAGGGGAAAACGTCAGTCAAGCTAGATATAGCCGCAGgtaaggagga ... ttttcttcagGAAGTGACGATAATGACATCATGAAGGTTTTTGGTAAGGGTGGTGCAGATG
EST: gi|71769071|gb|DR967008.1|DR967008
EST:     AGAACAGGTAGTGAAGGGGAAAACGTCAGTCAAGCTAGATATAGCCGCAG                         GAAGTGACGATAATGACATCATGAAGGTTTTTGGTAAGGGTGGTGCAGATG
genomic: AGAACAGGTAGTGAAGGGGAAAACGTCAGTCAAGCTAGATATAGCCGCAGgtaaggagga ... ttttcttcagGAAGTGACGATAATGACATCATGAAGGTTTTTGGTAAGGGTGGTGCAGATG
EST: gi|71427930|gb|DR808980.1|DR808980
EST:     AGAACAGGTAGTGAAGGGGAAAACGTCAGTCAAGCTAGATATAGCCGCAG                         GAAGTGACGATAATGACATCATGAAGGTTTTTGGTAAGGGTGGTGCAGATG
genomic: AGAACAGGTAGTGAAGGGGAAAACGTCAGTCAAGCTAGATATAGCCGCAGgtaaggagga ... ttttcttcagGAAGTGACGATAATGACATCATGAAGGTTTTTGGTAAGGGTGGTGCAGATG
EST: gi|37397730|gb|CF636173.1|CF636173
EST:     AGAACAGGTAGTGAAGGGGAAAACGTCAGTCAAGCTAGACATAGCCGCAG                         GAAGTGACGATAATGACATCATGAAGATTTTTGGTAAGGGTGGTGCAGATG
genomic: AGAACAGGTAGTGAAGGGGAAAACGTCAGTCAAGCTAGATATAGCCGCAGgtaaggagga ... ttttcttcagGAAGTGACGATAATGACATCATGAAGGTTTTTGGTAAGGGTGGTGCAGATG
EST: gi|32847340|gb|CD987021.1|CD987021
EST:     AGAACAGGTAGTGAAGGGGAAAACGTCAGTCAAGCTAGACATAGCCGCAG                         GAAGTGACGATAATGACATCATGAAGGTTTTTGGTAAGGGTGGTGCAGATG
genomic: AGAACAGGTAGTGAAGGGGAAAACGTCAGTCAAGCTAGATATAGCCGCAGgtaaggagga ... ttttcttcagGAAGTGACGATAATGACATCATGAAGGTTTTTGGTAAGGGTGGTGCAGATG
EST: gi|67040336|gb|CO466591.1|CO466591
EST:     AGAACAGGTAGTGAAGGGGAAAACGTCAGTCAAGCTAGACATAGCCGCAG                         GAAGTGACGATAATGACATCATGAAGGTTTTTGGTAAGGGTGGTGCAGATG
genomic: AGAACAGGTAGTGAAGGGGAAAACGTCAGTCAAGCTAGATATAGCCGCAGgtaaggagga ... ttttcttcagGAAGTGACGATAATGACATCATGAAGGTTTTTGGTAAGGGTGGTGCAGATG
EST: gi|40337178|gb|CK371248.1|CK371248
EST:     AGAACAGGTAGTGAAGGGGAAAACGTCAGTCAAGCTAGACATAGCCGCAG                         GAAGTGACGATAATGACATCATGAAGATTTTTGGTAAGGGTGGTGCAGATG
genomic: AGAACAGGTAGTGAAGGGGAAAACGTCAGTCAAGCTAGATATAGCCGCAGgtaaggagga ... ttttcttcagGAAGTGACGATAATGACATCATGAAGGTTTTTGGTAAGGGTGGTGCAGATG

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), 47 (downstream exon)
Score: 126

AGTTTTTGCAAGACTTGCAAAGGAGAACAGGTAGTGAAGGGGAAAACGTCAGTCAAGCTAGATATAGCCGCAGgtaaggagga ... ttttcttcagGAAGTGACGATAATGACATCATGAAGGTTTTTGGTAAGGGTGGTGCAGATGTTGACCGAAATAAGCCTGGTGACCTTTATGTTACTATCAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 110

AGTTTTTGCAAGACTTGCAAAGGAGAACAGGTAGTGAAGGGGAAAACGTCAGTCAAGCTAGATATAGCCGCAGgtaaggagga ... ttttcttcagGAAGTGACGATAATGACATCATGAAGGTTTTTGGTAAGGGTGGTGCAGATGTTGACCGAAATAAGCCTGGTGACCTTTATGTTACTATCAAG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 176

AGTTTTTGCAAGACTTGCAAAGGAGAACAGGTAGTGAAGGGGAAAACGTCAGTCAAGCTAGATATAGCCGCAGgtaaggagga ... ttttcttcagGAAGTGACGATAATGACATCATGAAGGTTTTTGGTAAGGGTGGTGCAGATGTTGACCGAAATAAGCCTGGTGACCTTTATGTTACTATCAAG


Block sizes: 46 (upstream exon), 47 (downstream exon)
Score: 91

AGTTTTTGCAAGACTTGCAAAGGAGAACAGGTAGTGAAGGGGAAAACGTCAGTCAAGCTAGATATAGCCGCAGgtaaggagga ... ttttcttcagGAAGTGACGATAATGACATCATGAAGGTTTTTGGTAAGGGTGGTGCAGATGTTGACCGAAATAAGCCTGGTGACCTTTATGTTACTATCAAG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AGTTTTTGCAAGACTTGCAAAGGAGAACAGGTAGTGAAGGGGAAAACGTCAGTCAAGCTAGATATAGCCGCAGgtaaggaggaattttctttactgatatatgtgtatgcttgacatgaactccatcccaaattataggttcttttggattttctaggtacatagcttgcacc

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