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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatattttctttcctttagtcctagaatattttccctcaaaagttactaaaacataactcagcatgcacaatgaatctttttcctgaaaagttactaaaacatgactcaccatgtgcagATGAATGATGGAAAGCCCACAGAGGAAGACGTAGAAGCTAAAATGGCACAAATGGTCTGTTCTTTTAACAACCGGGAAGAGTGCCTGGCGTGTGGAAGCT

Basic information

species Zea mays
transcript GRMZM2G340527_T01
intron # 16
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G340527_T01 (Zea mays), 3'ss of exon 16
lower sequence: LOC_Os06g07210.1 (Oryza sativa), 3'ss of exon 16
gtatattttctttcctttagtcctagaatattttccctcaaaagttactaaaacataactcagcatgcacaatgaatctttt----tcctgaaaagttactaaaacatgactcaccatgtgcagATGAATGATGGAAAGCCCACAGAGGAAG---ACGTAGAAGCTAAAATGGCACAAATGGTCTGTTCTTTTAACAACCGGGAAGAGTGCCTGGCGTGTGGAAGCT
                                                    |  |      ||   | | || | | ||||    ||||||| ||  |    | ||| |   |   ||| |||   || |     ||| |  |||||||||   |||| |||||||||||||| |||||||| ||||| || ||||||||||| |||||| ||||||||||||   
--------------------------------------------------gtatgtcttctggccctccccataattgttttacattcctgaatagccaactcaccattaaaaatattgttcagGAAAACGGCACCAAGGCTGCAGAGGAAGAGGACGTGGAAGCTAAAATGGCTCAAATGGTTTGTTCCTTGAACAACCGGGAGGAGTGCTTGGCGTGTGGAA---
















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|32931953|gb|CF036765.1|CF036765
EST:     CAATCAAGTTTACCGTCGATACCACACTTCTAAAGGAGAATGGGGATGGG                         ATGAATGATGGAAAGCCCACAGAGGAAGACGTAGAAGCTAAAATGGCACAA
genomic: CAATCAAGTTTACCGTCGATACCACACTTCTAAAGGAGAATGGGAATGGGgtatattttc ... ccatgtgcagATGAATGATGGAAAGCCCACAGAGGAAGACGTAGAAGCTAAAATGGCACAA
EST: gi|4621444|gb|AI612277.1|AI612277
EST:     CAATCAAGTTTACCGTCGATACCACACTTCTAAAGGAGAATGGGAATGGG                         ATGAATGATGGAAAGCCCACAGAGGAAGACGTAGAAGCTAAAATGGCACAA
genomic: CAATCAAGTTTACCGTCGATACCACACTTCTAAAGGAGAATGGGAATGGGgtatattttc ... ccatgtgcagATGAATGATGGAAAGCCCACAGAGGAAGACGTAGAAGCTAAAATGGCACAA
EST: gi|76015090|gb|DT942260.1|DT942260
EST:     CAATCAAGTTTACCGTCGATACCACACTTCTAAAGGAGAATGGGAATGGG                         ATGAATGATGGAAAGCCCACAGAGGAAGACGTAGAAGCTAAAATGGCACAA
genomic: CAATCAAGTTTACCGTCGATACCACACTTCTAAAGGAGAATGGGAATGGGgtatattttc ... ccatgtgcagATGAATGATGGAAAGCCCACAGAGGAAGACGTAGAAGCTAAAATGGCACAA
EST: gi|33091926|gb|CF051920.1|CF051920
EST:     CAATCAAGTTTACCGTCGATACCACACTTCTAAAGGAGAATGGGAATGGG                         ATGAATGATGGAAAGCCCACAGAGGAAGACGTAGAAGCTAAAATGGCACAA
genomic: CAATCAAGTTTACCGTCGATACCACACTTCTAAAGGAGAATGGGAATGGGgtatattttc ... ccatgtgcagATGAATGATGGAAAGCCCACAGAGGAAGACGTAGAAGCTAAAATGGCACAA
EST: gi|76018236|gb|DT945406.1|DT945406
EST:     CAATCAAGTTTACCGTCGATACCACACTTCTAAAGGAGAATGGGAATGGG                         ATGAATGATGGAAAGCCCACAGAGGAAGACGTAGAAGCTAAAATGGCACAA
genomic: CAATCAAGTTTACCGTCGATACCACACTTCTAAAGGAGAATGGGAATGGGgtatattttc ... ccatgtgcagATGAATGATGGAAAGCCCACAGAGGAAGACGTAGAAGCTAAAATGGCACAA
EST: gi|76921149|gb|DV168468.1|DV168468
EST:     CAATCAAGTTTACCGTCGATACCACACTTCTAAAGGAGAATGGGAATGGG                         ATGAATGATGGAAAGCCCACAGAGGAAGACGTAGAAGCTAAAATGGCACAA
genomic: CAATCAAGTTTACCGTCGATACCACACTTCTAAAGGAGAATGGGAATGGGgtatattttc ... ccatgtgcagATGAATGATGGAAAGCCCACAGAGGAAGACGTAGAAGCTAAAATGGCACAA
EST: gi|32933987|gb|CF038799.1|CF038799
EST:     CAATCAAGTTTACCGTCGATACCACACTTCTAAAGGAGAATGGGAATGGG                         ATGAATGATGGAAAGCCCACAGAGGAAGACGTAGAAGCTAAAATGGCACAA
genomic: CAATCAAGTTTACCGTCGATACCACACTTCTAAAGGAGAATGGGAATGGGgtatattttc ... ccatgtgcagATGAATGATGGAAAGCCCACAGAGGAAGACGTAGAAGCTAAAATGGCACAA
EST: gi|32930083|gb|CF034895.1|CF034895
EST:     CAATCAAGTTTACCGTCGATACCACACTTCTAAAGGAGAATGGGAATGGG                         ATGAATGATGGAAAGCCCACAGAGGAAGACGTAGAAGCTAAAATGGCACAA
genomic: CAATCAAGTTTACCGTCGATACCACACTTCTAAAGGAGAATGGGAATGGGgtatattttc ... ccatgtgcagATGAATGATGGAAAGCCCACAGAGGAAGACGTAGAAGCTAAAATGGCACAA
EST: gi|76921148|gb|DV168467.1|DV168467
EST:     CAATCAAGTTTACCGTCGATACCACACTTCTAAAGGAGAATGGGAATGGG                         ATGAATGATGGAAAGCCCACAGAGGAAGACGTAGAAGCTAAAATGGCACAA
genomic: CAATCAAGTTTACCGTCGATACCACACTTCTAAAGGAGAATGGGAATGGGgtatattttc ... ccatgtgcagATGAATGATGGAAAGCCCACAGAGGAAGACGTAGAAGCTAAAATGGCACAA

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: 46

GGCCTGAAAACTGGAATGTACTATCTACGCACACGAGCTGCTGCTGATGCAATCAAGTTTACCGTCGATACCACACTTCTAAAGGAGAATGGGAATGGGgtatattttc ... ccatgtgcagATGAATGATGGAAAGCCCACAGAGGAAGACGTAGAAGCTAAAATGGCACAAATGGTCTGTTCTTTTAACAACCGGGAAGAGTGCCTGGCGTGTGGAAGCT


Block sizes: 48 (upstream exon), 43 (downstream exon)
Score: 8

GGCCTGAAAACTGGAATGTACTATCTACGCACACGAGCTGCTGCTGATGCAATCAAGTTTACCGTCGATACCACACTTCTAAAGGAGAATGGGAATGGGgtatattttc ... ccatgtgcagATGAATGATGGAAAGCCCACAGAGGAAGACGTAGAAGCTAAAATGGCACAAATGGTCTGTTCTTTTAACAACCGGGAAGAGTGCCTGGCGTGTGGAAGCT


Block sizes: 38 (upstream exon), 33 (downstream exon)
Score: 4

GGCCTGAAAACTGGAATGTACTATCTACGCACACGAGCTGCTGCTGATGCAATCAAGTTTACCGTCGATACCACACTTCTAAAGGAGAATGGGAATGGGgtatattttc ... ccatgtgcagATGAATGATGGAAAGCCCACAGAGGAAGACGTAGAAGCTAAAATGGCACAAATGGTCTGTTCTTTTAACAACCGGGAAGAGTGCCTGGCGTGTGGAAGCT


Block sizes: 44 (upstream exon), 19 (downstream exon)
Score: 2

GGCCTGAAAACTGGAATGTACTATCTACGCACACGAGCTGCTGCTGATGCAATCAAGTTTACCGTCGATACCACACTTCTAAAGGAGAATGGGAATGGGgtatattttc ... ccatgtgcagATGAATGATGGAAAGCCCACAGAGGAAGACGTAGAAGCTAAAATGGCACAAATGGTCTGTTCTTTTAACAACCGGGAAGAGTGCCTGGCGTGTGGAAGCT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgcacaatgaatctttttcctgaaaagttactaaaacatgactcaccatgtgcagATGAATGATGGAAAGCCCACAGAGGAAGACGTAGAAGCTAAAATGGCACAAATGGTCTGTTCTTTTAACAACCGGGAAGAGTGCCTGGCGTGTGGAAGCT
                      aaaagttactaaaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatattttctttcctttagtcctagaatattttccctcaaaagttactaaaacataactcagcatgcacaatgaatctttttcctgaaaagttactaaaacatgactcaccatgtgcagATGAATGATGGAAAGCCCACAGAGGAAGACGTAGAAGCTAAAATGGCACAAATGGTCTGTTCTTTTAACAACCGGGAAGAGTGCCTGGCGTGTGGAAGCT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG