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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...acgctgttgttttggcacctgggaacgcttgagaaaaatgcagtgttggctttcgagcacacttgattttgagctcttacaacctaatgtctctgttcagGAAAGCTGATCATCATCGCAAACAACTGCCCTCCACTTAGGAAGTCTGAGATTGAGTACTACGCCATGCTGGCCAAAGTTAGTGTGCACCATTTCCACGG

Basic information

species Zea mays
transcript GRMZM2G044137_T01
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G044137_T02 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os05g41110.2 (Oryza sativa), 3'ss of exon 2
--acgctgt-tgttttggcacctgggaacgcttgagaaaaatgcagtgttggctttcgagca-cacttgattttgagctcttacaacctaatgtctctgttcagGAAAGCTGATCATCATCGCAAACAACTGCCCTCCACTTAGGAAGTCTGAGATTGAGTACTACGCCATGCTGGCCAAAGTTAGTGTGCACCATTTCCACGG
    | ||  ||  || |||  |   |||   | || ||| | |||  | || | |   |       ||||| |||  ||  |  || |  | | | |||| ||| |||||||| ||| | |||||||||||||||||||| |||||||||||||||||||| ||||||||| |||  |||||||| || ||||||||||| ||
tcgagttgaatgaatttgcagttat-aacatgt-aggaaatttcag-ataggttgtgttgtggtttctgattgtgacatca-atcacatcttttttatgtttagGGAAGCTGATTATCCTTGCAAACAACTGCCCTCCACTCAGGAAGTCTGAGATTGAGTATTACGCCATGTTGGGAAAAGTTAGCGTTCACCATTTCCATGG
















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|76013092|gb|DT940262.1|DT940262
EST:     GTACACCCTGGGCTACAAGACCGTCCTCAAGACGCTGCGCAACTCCAAGG                         GAAAGCTGATCATCATCGCAAACAACTGCCCTCCACTTAGGAAGTCTGAGA
genomic: GTACACCCTGGGCTACAAGACCGTCCTCAAGACGCTGCGCAACTCCAAGGgtatcgattc ... ctctgttcagGAAAGCTGATCATCATCGCAAACAACTGCCCTCCACTTAGGAAGTCTGAGA
EST: gi|211065202|gb|FL140848.1|FL140848
EST:     GTACACCCTGGGCTACAAGACCGTCCTCAAGACGCTGCGCAACTCCAAGG                         GAAAGCTGATCATCATCGCAAACAACTGCCCTCCACTTAGGAAGTCTGAGA
genomic: GTACACCCTGGGCTACAAGACCGTCCTCAAGACGCTGCGCAACTCCAAGGgtatcgattc ... ctctgttcagGAAAGCTGATCATCATCGCAAACAACTGCCCTCCACTTAGGAAGTCTGAGA
EST: gi|31406277|gb|CD485009.1|CD485009
EST:     GTACACCCTGGGCTACAAGACCGTCCTCAAGACGCTGCGCAACTCCAAGG                         GAAAGCTGATCATCATCGCAAACAACTGCCCTCCACTTAGGAAGTCTGAGA
genomic: GTACACCCTGGGCTACAAGACCGTCCTCAAGACGCTGCGCAACTCCAAGGgtatcgattc ... ctctgttcagGAAAGCTGATCATCATCGCAAACAACTGCCCTCCACTTAGGAAGTCTGAGA
EST: gi|91049094|gb|EB159512.1|EB159512
EST:     GTACACCCTGGGCTACAAGACCGTCCTCAAGACGCTGCGCAACTCCAAGG                         GAAAGCTGATCATCATCGCAAACAACTGCCCTCCACTTAGGAAGTCTGAGA
genomic: GTACACCCTGGGCTACAAGACCGTCCTCAAGACGCTGCGCAACTCCAAGGgtatcgattc ... ctctgttcagGAAAGCTGATCATCATCGCAAACAACTGCCCTCCACTTAGGAAGTCTGAGA
EST: gi|60394375|gb|DN227245.1|DN227245
EST:     GTACACCCTGGGCTACAAGACCGTCCTCAAGACGCTGCGCAACTCCAAGG                         GAAAGCTGATCATCATCGCAAACAACTGCCCTCCACTTAGGAAGTCTGAGA
genomic: GTACACCCTGGGCTACAAGACCGTCCTCAAGACGCTGCGCAACTCCAAGGgtatcgattc ... ctctgttcagGAAAGCTGATCATCATCGCAAACAACTGCCCTCCACTTAGGAAGTCTGAGA
EST: gi|60355557|gb|DN222530.1|DN222530
EST:     GTACACCCTGGGCTACAAGACCGTCCTCAAGACGCTGCGCAACTCCAAGG                         GAAAGCTGATCATCATCGCAAACAACTGCCCTCCACTTAGGAAGTCTGAGA
genomic: GTACACCCTGGGCTACAAGACCGTCCTCAAGACGCTGCGCAACTCCAAGGgtatcgattc ... ctctgttcagGAAAGCTGATCATCATCGCAAACAACTGCCCTCCACTTAGGAAGTCTGAGA
EST: gi|211067927|gb|FL140853.1|FL140853
EST:     GTACACCCTGGGCTACAAGACCGTCCTCAAGACGCTGCGCAACTCCAAGG                         GAAAGCTGATCATCATCGCAAACAACTGCCCTCCACTTAGGAAGTCTGAGA
genomic: GTACACCCTGGGCTACAAGACCGTCCTCAAGACGCTGCGCAACTCCAAGGgtatcgattc ... ctctgttcagGAAAGCTGATCATCATCGCAAACAACTGCCCTCCACTTAGGAAGTCTGAGA
EST: gi|67023955|gb|CO452704.1|CO452704
EST:     GTACACCCTGGGCTACAAGACCGTCCTCAAGACGCTGCGCAACTCCAAGG                         GAAAGCTGATCATCATCGCAAACAACTGCCCTCCACTTAGGAAGTCTGAGA
genomic: GTACACCCTGGGCTACAAGACCGTCCTCAAGACGCTGCGCAACTCCAAGGgtatcgattc ... ctctgttcagGAAAGCTGATCATCATCGCAAACAACTGCCCTCCACTTAGGAAGTCTGAGA
EST: gi|149089950|gb|EE179239.2|EE179239
EST:     GTACACCCTGGGCTACAAGACCGTCCTCAAGACGCTGCGCAACTCCAAGG                         GAAAGCTGATCATCATCGCAAACAACTGCCCTCCACTTAGGAAGTCTGAGA
genomic: GTACACCCTGGGCTACAAGACCGTCCTCAAGACGCTGCGCAACTCCAAGGgtatcgattc ... ctctgttcagGAAAGCTGATCATCATCGCAAACAACTGCCCTCCACTTAGGAAGTCTGAGA
EST: gi|32914523|gb|CF019335.1|CF019335
EST:     GTACACCCTGGGCTACAAGACCGTCCTCAAGACGCTGCGCAACTCCAAGG                         GAAAGCTGATCATCATCGCAAACAACTGCCCTCCACTTAGGAAGTCTGAGA
genomic: GTACACCCTGGGCTACAAGACCGTCCTCAAGACGCTGCGCAACTCCAAGGgtatcgattc ... ctctgttcagGAAAGCTGATCATCATCGCAAACAACTGCCCTCCACTTAGGAAGTCTGAGA
EST: gi|32865422|gb|CF005104.1|CF005104
EST:     GTACACCCTGGGCTACAAGACCGTCCTCAAGACGCTGCGCAACTCCAAGG                         GAAAGCTGATCATCATCGCAAACAACTGCCCTCCACTTAGGAAGTCTGAGA
genomic: GTACACCCTGGGCTACAAGACCGTCCTCAAGACGCTGCGCAACTCCAAGGgtatcgattc ... ctctgttcagGAAAGCTGATCATCATCGCAAACAACTGCCCTCCACTTAGGAAGTCTGAGA
EST: gi|60338522|gb|DN205495.1|DN205495
EST:     GTACACCCTGGGCTACAAGACCGTCCTCAAGACGCTGCGCAACTCCAAGG                         GAAAGCTGATCATCATCGCAAACAACTGCCCTCCACTTAGGAAGTCTGAGA
genomic: GTACACCCTGGGCTACAAGACCGTCCTCAAGACGCTGCGCAACTCCAAGGgtatcgattc ... ctctgttcagGAAAGCTGATCATCATCGCAAACAACTGCCCTCCACTTAGGAAGTCTGAGA
EST: gi|15100298|gb|BI396089.1|BI396089
EST:     GTACACCCTGGGCTACAAGACCGTCCTCAAGACGCTGCGCAACTCCAAGG                         GAAAGCTGATCATCATCGCAAACAACTGCCCTCCACTTAGGAAGTCTGAGA
genomic: GTACACCCTGGGCTACAAGACCGTCCTCAAGACGCTGCGCAACTCCAAGGgtatcgattc ... ctctgttcagGAAAGCTGATCATCATCGCAAACAACTGCCCTCCACTTAGGAAGTCTGAGA
EST: gi|9824981|gb|BE575183.1|BE575183
EST:     GTACACCCTGGGCTACAAGACCGTCCTCAAGACGCTGCGCAACTCCAAGG                         GAAAGCTGATCATCATCGCAAACAACTGCCCTCCACTTAGGAAGTCTGAGA
genomic: GTACACCCTGGGCTACAAGACCGTCCTCAAGACGCTGCGCAACTCCAAGGgtatcgattc ... ctctgttcagGAAAGCTGATCATCATCGCAAACAACTGCCCTCCACTTAGGAAGTCTGAGA
EST: gi|211067924|gb|FL140850.1|FL140850
EST:     GTACACCCTGGGCTACAAGACCGTCCTCAAGACGCTGCGCAACTCCAAGG                         GAAAGCTGATCATCATCGCAAACAACTGCCCTCCACTTAGGAAGTCTGAGA
genomic: GTACACCCTGGGCTACAAGACCGTCCTCAAGACGCTGCGCAACTCCAAGGgtatcgattc ... ctctgttcagGAAAGCTGATCATCATCGCAAACAACTGCCCTCCACTTAGGAAGTCTGAGA
EST: gi|89251915|gb|DY623701.1|DY623701
EST:     GTACACCCTGGGCTACAAGACCGTCCTCAAGACGCTGCGCAACTCCAAGG                         GAAAGCTGATCATCATCGCAAACAACTGCCCTCCACTTAGGAAGTCTGAGA
genomic: GTACACCCTGGGCTACAAGACCGTCCTCAAGACGCTGCGCAACTCCAAGGgtatcgattc ... ctctgttcagGAAAGCTGATCATCATCGCAAACAACTGCCCTCCACTTAGGAAGTCTGAGA
EST: gi|27575973|gb|CA998667.1|CA998667
EST:     GTACACCCTGGGCTACAAGACCGTCCTCAAGACGCTGCGCAACTCCAAGG                         GAAAGCTGATCATCATCGCAAACAACTGCCCTCCACTTAGGAAGTCTGAGA
genomic: GTACACCCTGGGCTACAAGACCGTCCTCAAGACGCTGCGCAACTCCAAGGgtatcgattc ... ctctgttcagGAAAGCTGATCATCATCGCAAACAACTGCCCTCCACTTAGGAAGTCTGAGA
EST: gi|31441073|gb|CD510504.1|CD510504
EST:     GTACACCCTGGGCTACAAGACCGTCCTCAAGACGCTGCGCAACTCCAAGG                         GAAAGCTGATCATCATCGCAAACAACTGCCCTCCACTTAGGAAGTCTGAGA
genomic: GTACACCCTGGGCTACAAGACCGTCCTCAAGACGCTGCGCAACTCCAAGGgtatcgattc ... ctctgttcagGAAAGCTGATCATCATCGCAAACAACTGCCCTCCACTTAGGAAGTCTGAGA
EST: gi|60357629|gb|DN224602.1|DN224602
EST:     GTACACCCTGGGCTACAAGACCGTCCTCAAGACGCTGCGCAACTCCAAGG                         GAAAGCTGATCATCATCGCAAACAACTGCCCTCCACTTAGGAAGTCTGAGA
genomic: GTACACCCTGGGCTACAAGACCGTCCTCAAGACGCTGCGCAACTCCAAGGgtatcgattc ... ctctgttcagGAAAGCTGATCATCATCGCAAACAACTGCCCTCCACTTAGGAAGTCTGAGA
EST: gi|211065201|gb|FL140847.1|FL140847
EST:     GTACACCCTGGGCTACAAGACCGTCCTCAAGACGCTGCGCAACTCCAAGG                         GAAAGCTGATCATCATCGCAAACAACTGCCCTCCACTTAGGAAGTCTGAGA
genomic: GTACACCCTGGGCTACAAGACCGTCCTCAAGACGCTGCGCAACTCCAAGGgtatcgattc ... ctctgttcagGAAAGCTGATCATCATCGCAAACAACTGCCCTCCACTTAGGAAGTCTGAGA
EST: gi|71299866|gb|DR785955.1|DR785955
EST:     GTACACCCTGGGCTACAAGACCGTCCTCAAGACGCTGCGCAACTCCAAGG                         GAAAGCTGATCATCATCGCAAACAACTGCCCTCCACTTAGGAAGTTTGAGA
genomic: GTACACCCTGGGCTACAAGACCGTCCTCAAGACGCTGCGCAACTCCAAGGgtatcgattc ... ctctgttcagGAAAGCTGATCATCATCGCAAACAACTGCCCTCCACTTAGGAAGTCTGAGA
EST: gi|60341097|gb|DN208070.1|DN208070
EST:     GTACACCCTGGGCTACAAGACCGTCCTCAAGACGCTGCGCAACTCCAAGG                         GAAAGCTGATCATCATCGCAAACAACTGCCCTCCACTTAGGAAGTCTGAGA
genomic: GTACACCCTGGGCTACAAGACCGTCCTCAAGACGCTGCGCAACTCCAAGGgtatcgattc ... ctctgttcagGAAAGCTGATCATCATCGCAAACAACTGCCCTCCACTTAGGAAGTCTGAGA
EST: gi|60347030|gb|DN214003.1|DN214003
EST:     GTACACCCTGGGCTACAAGACCGTCCTCAAGACGCTGCGCAACTCCAAGG                         GAAAGCTGATCATCATCGCAAACAACTGCCCTCCACTTAGGAAGTCTGAGA
genomic: GTACACCCTGGGCTACAAGACCGTCCTCAAGACGCTGCGCAACTCCAAGGgtatcgattc ... ctctgttcagGAAAGCTGATCATCATCGCAAACAACTGCCCTCCACTTAGGAAGTCTGAGA

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: 2161

AGCACAGAGAGCATCAACAACAAGCTGCAGCTGGTGATGAAGAGCGGCAAGTACACCCTGGGCTACAAGACCGTCCTCAAGACGCTGCGCAACTCCAAGGgtatcgattc ... ctctgttcagGAAAGCTGATCATCATCGCAAACAACTGCCCTCCACTTAGGAAGTCTGAGATTGAGTACTACGCCATGCTGGCCAAAGTTAGTGTGCACCATTTCCACGG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 1827

AGCACAGAGAGCATCAACAACAAGCTGCAGCTGGTGATGAAGAGCGGCAAGTACACCCTGGGCTACAAGACCGTCCTCAAGACGCTGCGCAACTCCAAGGgtatcgattc ... ctctgttcagGAAAGCTGATCATCATCGCAAACAACTGCCCTCCACTTAGGAAGTCTGAGATTGAGTACTACGCCATGCTGGCCAAAGTTAGTGTGCACCATTTCCACGG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 1339

AGCACAGAGAGCATCAACAACAAGCTGCAGCTGGTGATGAAGAGCGGCAAGTACACCCTGGGCTACAAGACCGTCCTCAAGACGCTGCGCAACTCCAAGGgtatcgattc ... ctctgttcagGAAAGCTGATCATCATCGCAAACAACTGCCCTCCACTTAGGAAGTCTGAGATTGAGTACTACGCCATGCTGGCCAAAGTTAGTGTGCACCATTTCCACGG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 1109

AGCACAGAGAGCATCAACAACAAGCTGCAGCTGGTGATGAAGAGCGGCAAGTACACCCTGGGCTACAAGACCGTCCTCAAGACGCTGCGCAACTCCAAGGgtatcgattc ... ctctgttcagGAAAGCTGATCATCATCGCAAACAACTGCCCTCCACTTAGGAAGTCTGAGATTGAGTACTACGCCATGCTGGCCAAAGTTAGTGTGCACCATTTCCACGG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttggctttcgagcacacttgattttgagctcttacaacctaatgtctctgttcagGAAAGCTGATCATCATCGCAAACAACTGCCCTCCACTTAGGAAGTCTGAGATTGAGTACTACGCCATGCTGGCCAAAGTTAGTGTGCACCATTTCCACGG
                                    acctaat  putative branch site (score: 1109)
                                            tctctgttc  CT-rich tract
                 ttgatttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
acgctgttgttttggcacctgggaacgcttgagaaaaatgcagtgttggctttcgagcacacttgattttgagctcttacaacctaatgtctctgttcagGAAAGCTGATCATCATCGCAAACAACTGCCCTCCACTTAGGAAGTCTGAGATTGAGTACTACGCCATGCTGGCCAAAGTTAGTGTGCACCATTTCCACGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  ATGCTG