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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...atagattttattgtttggaagcaattgggaaaacattatttacttttaaaatatttgctgcatacttgtatttaaataacacttgccctttcttgaacagAGTTGGCGCAACTGACAGGAATAGCGGCTATACTTCGTTTTCCTCTTCCTGAACTAGAGGACATGGAGCTGTGATGAAACCAACCTTTTTGCTTCTCGAT

Basic information

species Zea mays
transcript GRMZM2G044011_T01
intron # 15
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G044011_T02 (Zea mays), 3'ss of exon 14
lower sequence: LOC_Os04g56480.2 (Oryza sativa), 3'ss of exon 14
--------------------------------------------------------------------------------atagattttattgtttggaagcaattgggaaaacattatttacttttaaaatatttgctgcatact------tgtatttaaataacacttgcccttt---cttgaacagAGTTGGCGCAACTGACAGGAATAGCGGCTATACTTCGTTTTCCTCTTCCTGAACTAGAGGACATGGAGCTGTGATGAAACCAACCTTTTTGCTTCTCGAT
                                                                                 |  || |||   |||   | |||       |  | | | || |||  |    ||||||||||  |      ||| |||||     | ||    |||    |||| |||||||||||||  |||||||||| || ||||||||||| |||||  | || ||  |||||||||| ||| |||||| |  ||| | ||     ||  | ||
gtaagtattcgtatccatttgtacttcactataactgctcatcaaaatgcaatagaccagttcataaataattgtcacattttcatattaacctttttgaacaaggaatttattaatttgtaatttgcattagtttgctgcattgtgttctctgtgtttaaggtggatttttttttttcatttgagcagAGTTGGCGCAGTTGACAGGAATCGCAGCTATACTTCGATTTCCCTTGCCAGATTTAGAGGACATTGAGATGTGATAATTCCACCGTTCAGAATTGGCAAT
















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|67018038|gb|CO446787.1|CO446787
EST:     AAATAGTGGCACAGTACACATATTTTCCTCGATGCATGTCTCGGGCGAAC                         AGTTGGCGCAACTGACAGGAATAGCGGCTATACTTCGTTTTCCCCTTCCTG
genomic: AAATAGTGGCACAGTACACATATTTTCCTCGATGCATGTCTCGGGCGAACgtgagtactt ... tcttgaacagAGTTGGCGCAACTGACAGGAATAGCGGCTATACTTCGTTTTCCTCTTCCTG
EST: gi|211495349|gb|FL234479.1|FL234479
EST:     AAATAGTGGCACAGTACACATATTTTCCTCGATGCATGTCTCGGGCGAAC                         AGTTGGCGCAACTGACAGGAATAGCAGCTATACTTCGTTTTCCCCTTCCTG
genomic: AAATAGTGGCACAGTACACATATTTTCCTCGATGCATGTCTCGGGCGAACgtgagtactt ... tcttgaacagAGTTGGCGCAACTGACAGGAATAGCGGCTATACTTCGTTTTCCTCTTCCTG
EST: gi|91048656|gb|EB159074.1|EB159074
EST:     AAATAGTGGCACAGTACACATATTTTCCTCGATGCATGTCTCGGGCGAAC                         AGTTGGCGCAACTGACAGGAATAGCGGCTATACTTCGTTTTCCTCTTCCTG
genomic: AAATAGTGGCACAGTACACATATTTTCCTCGATGCATGTCTCGGGCGAACgtgagtactt ... tcttgaacagAGTTGGCGCAACTGACAGGAATAGCGGCTATACTTCGTTTTCCTCTTCCTG
EST: gi|67018605|gb|CO447354.1|CO447354
EST:     AAATAGTGGCACAGTACACATATTTTCCTCGATGCATGTCTCGGGCGAAC                         AGTTGGCGCAACTGACAGGAATAGCGGCTATACTTCGTTTTCCCCTTCCTG
genomic: AAATAGTGGCACAGTACACATATTTTCCTCGATGCATGTCTCGGGCGAACgtgagtactt ... tcttgaacagAGTTGGCGCAACTGACAGGAATAGCGGCTATACTTCGTTTTCCTCTTCCTG
EST: gi|67024357|gb|CO453106.1|CO453106
EST:     AAATAGTGGCACAGTACACATATTTTCCTCGATGCATGTCTCGGGCGAAC                         AGTTGGCGCAACTGACAGGAATAGCGGCTATACTTCGTTNTCC-CTTCCTG
genomic: AAATAGTGGCACAGTACACATATTTTCCTCGATGCATGTCTCGGGCGAACgtgagtactt ... tcttgaacagAGTTGGCGCAACTGACAGGAATAGCGGCTATACTTCGTTTTCCTCTTCCTG
EST: gi|40303701|gb|CK348088.1|CK348088
EST:     AAATAGTGGCACAGTACACATATTTTCCTCGATGCATGTCTCGGGCGAAC                         AGTTGGCGCAACTGACAGGAATAGCGGCTATACTTCGTTTTCCTCTTCCTG
genomic: AAATAGTGGCACAGTACACATATTTTCCTCGATGCATGTCTCGGGCGAACgtgagtactt ... tcttgaacagAGTTGGCGCAACTGACAGGAATAGCGGCTATACTTCGTTTTCCTCTTCCTG
EST: gi|33092927|gb|CF052921.1|CF052921
EST:     TACACATATTTTCCTCGATGCATGTCTCGGGCGAAC                         AGTTGGCGCAACTGACAGGAATAGCGGCTATACTTCGTTTTCCTCTTCCTG
genomic: TACACATATTTTCCTCGATGCATGTCTCGGGCGAACgtgagtactt ... tcttgaacagAGTTGGCGCAACTGACAGGAATAGCGGCTATACTTCGTTTTCCTCTTCCTG
EST: gi|71763506|gb|DR961443.1|DR961443
EST:     AAATAGTGGCACAGTACACATATTTTCCTCGATGCATGTCTCGGGCGAAC                         AGTTGGCGCAACTGACAGGAATAGCGGCTATACTTCGTTTTCCTCTTCCTG
genomic: AAATAGTGGCACAGTACACATATTTTCCTCGATGCATGTCTCGGGCGAACgtgagtactt ... tcttgaacagAGTTGGCGCAACTGACAGGAATAGCGGCTATACTTCGTTTTCCTCTTCCTG
EST: gi|74236267|gb|DT644181.1|DT644181
EST:     AAATAGTGGCACAGTACACATATTTTCCTCGATGCATGTCTCGGGGGAAC                         AGTTGGCGCAACTGACAGGAATAGCGGCTATACTTCGTTTTCCTCTTCCTG
genomic: AAATAGTGGCACAGTACACATATTTTCCTCGATGCATGTCTCGGGCGAACgtgagtactt ... tcttgaacagAGTTGGCGCAACTGACAGGAATAGCGGCTATACTTCGTTTTCCTCTTCCTG
EST: gi|211359052|gb|FL430699.1|FL430699
EST:     AAATAGTGGCACAGTACACATATTTTCCTCGATGCATGTCTCGGGCGAAC                         AGTTGGCGCAACTGACAGGAATAGCAGCTATACTTCGTTTTCCCCTTCCTG
genomic: AAATAGTGGCACAGTACACATATTTTCCTCGATGCATGTCTCGGGCGAACgtgagtactt ... tcttgaacagAGTTGGCGCAACTGACAGGAATAGCGGCTATACTTCGTTTTCCTCTTCCTG
EST: gi|71442136|gb|DR823186.1|DR823186
EST:     AAATAGTGGCACAGTACACATATTTTCCTCGATGCATGTCTCGGGCGAAC                         AGTTGGCGCAACTGACAGGAATAGCGGCTATACTTCGTTTTCCTCTTCCTG
genomic: AAATAGTGGCACAGTACACATATTTTCCTCGATGCATGTCTCGGGCGAACgtgagtactt ... tcttgaacagAGTTGGCGCAACTGACAGGAATAGCGGCTATACTTCGTTTTCCTCTTCCTG
EST: gi|50333168|gb|CO528294.1|CO528294
EST:     AAATAGTGGCACAGTACACATATTTTCCTCGATGCATGTCTCGGGCGAAC                         AGTTGGCGCAACTGACAGGAATAGCGGCTATACTTCGTTTTCCTCTTCCTG
genomic: AAATAGTGGCACAGTACACATATTTTCCTCGATGCATGTCTCGGGCGAACgtgagtactt ... tcttgaacagAGTTGGCGCAACTGACAGGAATAGCGGCTATACTTCGTTTTCCTCTTCCTG
EST: gi|67021632|gb|CO450381.1|CO450381
EST:     AAATAGTGGCACAGTACACATATTTTCCTCGATGCATGTCTCGGGCGAAC                         ATTTGGCGCAACTGACAGGAATAGCGGCTATACTTCGTTTTCCCCTTCCTG
genomic: AAATAGTGGCACAGTACACATATTTTCCTCGATGCATGTCTCGGGCGAACgtgagtactt ... tcttgaacagAGTTGGCGCAACTGACAGGAATAGCGGCTATACTTCGTTTTCCTCTTCCTG
EST: gi|71302744|gb|DR787484.1|DR787484
EST:     AAATAGTGGCACAGTACACATATTTTCCTCGATGCATGTCTCGGGCGAAC                         AGTTGGCGCAACTGACAGGAATAGCGGCTATACTTCGTTTTCCTCTTCCTG
genomic: AAATAGTGGCACAGTACACATATTTTCCTCGATGCATGTCTCGGGCGAACgtgagtactt ... tcttgaacagAGTTGGCGCAACTGACAGGAATAGCGGCTATACTTCGTTTTCCTCTTCCTG
EST: gi|76016282|gb|DT943452.1|DT943452
EST:     AAATAGTGGCACAGTACACATATTTTCCTCGATGCATGTCTCGGGCGAAC                         AGTTGGCGCAACTGACAGGAATAGCGGCTATACTTCGTTTTCCTCTTCCTG
genomic: AAATAGTGGCACAGTACACATATTTTCCTCGATGCATGTCTCGGGCGAACgtgagtactt ... tcttgaacagAGTTGGCGCAACTGACAGGAATAGCGGCTATACTTCGTTTTCCTCTTCCTG

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), 45 (downstream exon)
Score: 62

GACATTGCTACGAGGCAAAGGTACGTGAAGTTGGTTGAAGATGTCAAGAAAAATAGTGGCACAGTACACATATTTTCCTCGATGCATGTCTCGGGCGAACgtgagtactt ... tcttgaacagAGTTGGCGCAACTGACAGGAATAGCGGCTATACTTCGTTTTCCTCTTCCTGAACTAGAGGACATGGAGCTGTGATGAAACCAACCTTTTTGCTTCTCGAT


Block sizes: 49 (upstream exon), 42 (downstream exon)
Score: 149

GACATTGCTACGAGGCAAAGGTACGTGAAGTTGGTTGAAGATGTCAAGAAAAATAGTGGCACAGTACACATATTTTCCTCGATGCATGTCTCGGGCGAACgtgagtactt ... tcttgaacagAGTTGGCGCAACTGACAGGAATAGCGGCTATACTTCGTTTTCCTCTTCCTGAACTAGAGGACATGGAGCTGTGATGAAACCAACCTTTTTGCTTCTCGAT


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 79

GACATTGCTACGAGGCAAAGGTACGTGAAGTTGGTTGAAGATGTCAAGAAAAATAGTGGCACAGTACACATATTTTCCTCGATGCATGTCTCGGGCGAACgtgagtactt ... tcttgaacagAGTTGGCGCAACTGACAGGAATAGCGGCTATACTTCGTTTTCCTCTTCCTGAACTAGAGGACATGGAGCTGTGATGAAACCAACCTTTTTGCTTCTCGAT


Block sizes: 46 (upstream exon), 49 (downstream exon)
Score: 63

GACATTGCTACGAGGCAAAGGTACGTGAAGTTGGTTGAAGATGTCAAGAAAAATAGTGGCACAGTACACATATTTTCCTCGATGCATGTCTCGGGCGAACgtgagtactt ... tcttgaacagAGTTGGCGCAACTGACAGGAATAGCGGCTATACTTCGTTTTCCTCTTCCTGAACTAGAGGACATGGAGCTGTGATGAAACCAACCTTTTTGCTTCTCGAT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttaaaatatttgctgcatacttgtatttaaataacacttgccctttcttgaacagAGTTGGCGCAACTGACAGGAATAGCGGCTATACTTCGTTTTCCTCTTCCTGAACTAGAGGACATGGAGCTGTGATGAAACCAACCTTTTTGCTTCTCGAT
                            aaataac  putative branch site (score: 63)
                                  cacttgccctttctt  CT-rich tract
                atacttgtatttaaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
atagattttattgtttggaagcaattgggaaaacattatttacttttaaaatatttgctgcatacttgtatttaaataacacttgccctttcttgaacagAGTTGGCGCAACTGACAGGAATAGCGGCTATACTTCGTTTTCCTCTTCCTGAACTAGAGGACATGGAGCTGTGATGAAACCAACCTTTTTGCTTCTCGAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCT