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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtcatcctgtcacgtgaaacttgtatacacagatagatgagtgtaaaataaattgttgaattgaatgtagGTGCTGTTGTCGAAGCTACCAGATGGTGGTGAGAAGATAAGGAGGCAGATAAATGAGCTGGACGAGAAGCTGACTTCTGCTGAGAAGGGGCTGAAGGAGG

Basic information

species Zea mays
transcript GRMZM2G138125_T01
intron # 19
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G138125_T01 (Zea mays), 3'ss of exon 19
lower sequence: LOC_Os04g59624.2 (Oryza sativa), 3'ss of exon 19
---------------gtaagtcatcctgtcacgtgaaacttgtatacacagatagatgagtgtaaaataaattgttgaattgaatgtagGTGCTGTTGTCGAAGCTACCAGATGGTGGTGAGAAGATAAGGAGGCAGATAAATGAGCTGGACGAGAAGCTGACTTCTGCTGAGAAGGGGCTGAAGGAGG
                 |    | |||||  | || | |||||         |   |  || | | |  | |||  |   |   ||||||||||  || |||||||||||||| |||| || |||||||||||||||||||||||||||||||| ||||||||       |||      | | ||    
gtgggagcaagaaagacacccgaacctgttgcatgcatcttgtggtgtgttgtctgtctgtcttacaccatttgccgctgt---tgtagGTGCTTGTGGCGAAGCTACCAGATCGTGGAGACAAGATAAGGAGGCAGATAAATGAGCTGGACGAAAAGCTGACCGTGATCGAGTCTTCTCCGGAGCCAT
















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|5525254|gb|AI861093.1|AI861093
EST:     AAGAGATAAAGGCAAGAATCAACCGGCTTTCACAGACCCTCTCCAACGCT                         GTGCTGTTGTCGAAGCTACCAGATGGTGGTGAGAAGATAAGGAGGCAGATA
genomic: AAGAGATAAAGGCAAGAATCAACCGGCTTTCACAGACCCTCTCCAACGCTgtaagtcatc ... ttgaatgtagGTGCTGTTGTCGAAGCTACCAGATGGTGGTGAGAAGATAAGGAGGCAGATA
EST: gi|32930747|gb|CF035559.1|CF035559
EST:     AAGAGATAAAGGCAAGAATCAACCGGCTTTCACAGACCCTCTCCAACGCT                         GTGCTGTTGTCGAAGCTACCAGATGGTGGTGAGAAGATAAGGAGGCAGATA
genomic: AAGAGATAAAGGCAAGAATCAACCGGCTTTCACAGACCCTCTCCAACGCTgtaagtcatc ... ttgaatgtagGTGCTGTTGTCGAAGCTACCAGATGGTGGTGAGAAGATAAGGAGGCAGATA
EST: gi|67034321|gb|CO462871.1|CO462871
EST:     AAGAGATAAAGGCAAGAATCAACCGGCTTTCACAGACCCTCTCCAACGCT                         GTGCTGTTGTCGAAGCTACCAGATGGTGGTGAGAAGATAAGGAGGCAGATA
genomic: AAGAGATAAAGGCAAGAATCAACCGGCTTTCACAGACCCTCTCCAACGCTgtaagtcatc ... ttgaatgtagGTGCTGTTGTCGAAGCTACCAGATGGTGGTGAGAAGATAAGGAGGCAGATA
EST: gi|29130029|gb|CB380733.1|CB380733
EST:     AAGAGATAAAGGCAAGAATCAACCGGCTTTCACAGACCCTCTCCAACGCT                         GTGCTGTTGTCGAAGCTACCAGATGGTGGTGAGAAGATAAGGAGGCAGATA
genomic: AAGAGATAAAGGCAAGAATCAACCGGCTTTCACAGACCCTCTCCAACGCTgtaagtcatc ... ttgaatgtagGTGCTGTTGTCGAAGCTACCAGATGGTGGTGAGAAGATAAGGAGGCAGATA
EST: gi|32937709|gb|CF042528.1|CF042528
EST:     GGCTTTCACAGACCCTCTCCAACGCT                         GTGCTGTTGTCGAAGCTACCAGATGGTGGTGAGAAGATAAGGAGGCAGATA
genomic: GGCTTTCACAGACCCTCTCCAACGCTgtaagtcatc ... ttgaatgtagGTGCTGTTGTCGAAGCTACCAGATGGTGGTGAGAAGATAAGGAGGCAGATA
EST: gi|28873895|gb|CB329824.1|CB329824
EST:     AAGAGATAAAGGCAAGAATCAACCGGCTTTCACAGACCCTCTCCAACGCT                         GTGCTGTTGTCGAAGCTACCCGATGGTGGTGAGAAGATAAGGAGGCAGATA
genomic: AAGAGATAAAGGCAAGAATCAACCGGCTTTCACAGACCCTCTCCAACGCTgtaagtcatc ... ttgaatgtagGTGCTGTTGTCGAAGCTACCAGATGGTGGTGAGAAGATAAGGAGGCAGATA
EST: gi|33091324|gb|CF051318.1|CF051318
EST:     AAGAGATAAAGGCAAGAATCAACCGGCTTTCACAGACCCTCTCCAACGCT                         GTGCTGTTGTCGAAGCTACCAGATGGTGGTGAGAAGATAAGGAGGCAGATA
genomic: AAGAGATAAAGGCAAGAATCAACCGGCTTTCACAGACCCTCTCCAACGCTgtaagtcatc ... ttgaatgtagGTGCTGTTGTCGAAGCTACCAGATGGTGGTGAGAAGATAAGGAGGCAGATA
EST: gi|67020146|gb|CO448895.1|CO448895
EST:     AAGAGATAAAGGCAAGAATCAACCGGCTTTCACAGACCCTCTCCAACGCT                         GTGCTGTTGTCGAAGCTACCAGATGGTGGTGAGAAGATAAGGAGGCAGATA
genomic: AAGAGATAAAGGCAAGAATCAACCGGCTTTCACAGACCCTCTCCAACGCTgtaagtcatc ... ttgaatgtagGTGCTGTTGTCGAAGCTACCAGATGGTGGTGAGAAGATAAGGAGGCAGATA
EST: gi|67018670|gb|CO447419.1|CO447419
EST:     AAGAGATAAAGGCAAGAATCAACCGGCTTTCACAGACCCTCTCCAACGCT                         GTGCTGTTGTCGAAGCTACCAGATGGTGGTGAGAAGATAAGGAGGCAGATA
genomic: AAGAGATAAAGGCAAGAATCAACCGGCTTTCACAGACCCTCTCCAACGCTgtaagtcatc ... ttgaatgtagGTGCTGTTGTCGAAGCTACCAGATGGTGGTGAGAAGATAAGGAGGCAGATA
EST: gi|32936941|gb|CF041760.1|CF041760
EST:     AAGAGATAAAGGCAAGAATCAACCGGCTTTCACAGACCCTCTCCAACGCT                         GTGCTGTTGTCGAAGCTACCAGATGGTGGTGAGAAGATAAGGAGGCAGATA
genomic: AAGAGATAAAGGCAAGAATCAACCGGCTTTCACAGACCCTCTCCAACGCTgtaagtcatc ... ttgaatgtagGTGCTGTTGTCGAAGCTACCAGATGGTGGTGAGAAGATAAGGAGGCAGATA
EST: gi|32937325|gb|CF042144.1|CF042144
EST:     AAGAGATAAAGGCAAGAATCAACCGGCTTTCACAGACCCTCTCCAACGCT                         GTGCTGTTGTCGAAGCTACCAGATGGTGGTGAGAAGATAAGGAGGCAGATA
genomic: AAGAGATAAAGGCAAGAATCAACCGGCTTTCACAGACCCTCTCCAACGCTgtaagtcatc ... ttgaatgtagGTGCTGTTGTCGAAGCTACCAGATGGTGGTGAGAAGATAAGGAGGCAGATA
EST: gi|71419756|gb|DR804887.1|DR804887
EST:     AAGAGATAAAGGCAAGAATCAACCGGCTTTCACAGACCCTCTCCAACGCT                         GTGCTGTTGTCGAAGCTACCAGATGGTGGTGAGAAGATAAGGAGGCAGATA
genomic: AAGAGATAAAGGCAAGAATCAACCGGCTTTCACAGACCCTCTCCAACGCTgtaagtcatc ... ttgaatgtagGTGCTGTTGTCGAAGCTACCAGATGGTGGTGAGAAGATAAGGAGGCAGATA
EST: gi|5058783|gb|AI737259.1|AI737259
EST:     AAGAGATAAAGGCAAGAATCANCCGGCTTTCNCAGACCCTCTCCAACGCT                         GTGCTGTTGTCGAAGCTACCAGATGGTGGTGAGAAGATAAGGAGCCAGATA
genomic: AAGAGATAAAGGCAAGAATCAACCGGCTTTCACAGACCCTCTCCAACGCTgtaagtcatc ... ttgaatgtagGTGCTGTTGTCGAAGCTACCAGATGGTGGTGAGAAGATAAGGAGGCAGATA
EST: gi|71419751|gb|DR804886.1|DR804886
EST:     AAGAGATAAAGGCAAGAATCAACCGGCTTTCACAGACCCTCTCCAACGCT                         GTGCTGTTGTCGAAGCTACCAGATGGTGGTGAGAAGATAAGGAGGCAGATA
genomic: AAGAGATAAAGGCAAGAATCAACCGGCTTTCACAGACCCTCTCCAACGCTgtaagtcatc ... ttgaatgtagGTGCTGTTGTCGAAGCTACCAGATGGTGGTGAGAAGATAAGGAGGCAGATA
EST: gi|31909601|gb|CD651000.1|CD651000
EST:     AAGAGATAAAGGCAAGAATCAACCGGCTTTCACAGACCCTCTCCAACGCT                         GTGCTGTTGTCGAAGCTACCAGATGGTGGTGAGAAGATAAGGAGGCAGATA
genomic: AAGAGATAAAGGCAAGAATCAACCGGCTTTCACAGACCCTCTCCAACGCTgtaagtcatc ... ttgaatgtagGTGCTGTTGTCGAAGCTACCAGATGGTGGTGAGAAGATAAGGAGGCAGATA
EST: gi|60355698|gb|DN222671.1|DN222671
EST:     AAGAGATAAAGGCAAGAATCAACCGGCTTTCACAGACCCTCTCCAACGCT                         GTGCTGTTGTCGAAGCTACCAGATGGTGGTGAGAAGATAAGGAGGCAGATA
genomic: AAGAGATAAAGGCAAGAATCAACCGGCTTTCACAGACCCTCTCCAACGCTgtaagtcatc ... ttgaatgtagGTGCTGTTGTCGAAGCTACCAGATGGTGGTGAGAAGATAAGGAGGCAGATA
EST: gi|32930746|gb|CF035558.1|CF035558
EST:     AAGAGATAAAGGCAAGAATCAACCGGCTTTCACAGACCCTCTCCAACGCT                         GTGCTGTTGTCGAAGCTACCAGATGGTGGTGAGAAGATAAGGAGGCAGATA
genomic: AAGAGATAAAGGCAAGAATCAACCGGCTTTCACAGACCCTCTCCAACGCTgtaagtcatc ... ttgaatgtagGTGCTGTTGTCGAAGCTACCAGATGGTGGTGAGAAGATAAGGAGGCAGATA
EST: gi|60394842|gb|DN227711.1|DN227711
EST:     AAGAGATAAAGGCAAGAATCAACCGGCTTTCACAGACCCTCTCCAACGCT                         GTGCTGTTGTCGAAGCTACCAGATGGTGGTGAGAAGATAAGGAGGCAGATA
genomic: AAGAGATAAAGGCAAGAATCAACCGGCTTTCACAGACCCTCTCCAACGCTgtaagtcatc ... ttgaatgtagGTGCTGTTGTCGAAGCTACCAGATGGTGGTGAGAAGATAAGGAGGCAGATA

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), 48 (downstream exon)
Score: 147

TTTCACTGTTCGAAACTACATTCCAAGTAACAGAAGCGCAGAGAGTCCTGAAGAGATAAAGGCAAGAATCAACCGGCTTTCACAGACCCTCTCCAACGCTgtaagtcatc ... ttgaatgtagGTGCTGTTGTCGAAGCTACCAGATGGTGGTGAGAAGATAAGGAGGCAGATAAATGAGCTGGACGAGAAGCTGACTTCTGCTGAGAAGGGGCTGAAGGAGG


Block sizes: 45 (upstream exon), 46 (downstream exon)
Score: 40

TTTCACTGTTCGAAACTACATTCCAAGTAACAGAAGCGCAGAGAGTCCTGAAGAGATAAAGGCAAGAATCAACCGGCTTTCACAGACCCTCTCCAACGCTgtaagtcatc ... ttgaatgtagGTGCTGTTGTCGAAGCTACCAGATGGTGGTGAGAAGATAAGGAGGCAGATAAATGAGCTGGACGAGAAGCTGACTTCTGCTGAGAAGGGGCTGAAGGAGG


Block sizes: 48 (upstream exon), 48 (downstream exon)
Score: 32

TTTCACTGTTCGAAACTACATTCCAAGTAACAGAAGCGCAGAGAGTCCTGAAGAGATAAAGGCAAGAATCAACCGGCTTTCACAGACCCTCTCCAACGCTgtaagtcatc ... ttgaatgtagGTGCTGTTGTCGAAGCTACCAGATGGTGGTGAGAAGATAAGGAGGCAGATAAATGAGCTGGACGAGAAGCTGACTTCTGCTGAGAAGGGGCTGAAGGAGG


Block sizes: 40 (upstream exon), 47 (downstream exon)
Score: 36

TTTCACTGTTCGAAACTACATTCCAAGTAACAGAAGCGCAGAGAGTCCTGAAGAGATAAAGGCAAGAATCAACCGGCTTTCACAGACCCTCTCCAACGCTgtaagtcatc ... ttgaatgtagGTGCTGTTGTCGAAGCTACCAGATGGTGGTGAGAAGATAAGGAGGCAGATAAATGAGCTGGACGAGAAGCTGACTTCTGCTGAGAAGGGGCTGAAGGAGG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gaaacttgtatacacagatagatgagtgtaaaataaattgttgaattgaatgtagGTGCTGTTGTCGAAGCTACCAGATGGTGGTGAGAAGATAAGGAGGCAGATAAATGAGCTGGACGAGAAGCTGACTTCTGCTGAGAAGGGGCTGAAGGAGG
                            taaaataaattgttga  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagtcatcctgtcacgtgaaacttgtatacacagatagatgagtgtaaaataaattgttgaattgaatgtagGTGCTGTTGTCGAAGCTACCAGATGGTGGTGAGAAGATAAGGAGGCAGATAAATGAGCTGGACGAGAAGCTGACTTCTGCTGAGAAGGGGCTGAAGGAGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAG