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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...actgcacatcattatattaagaagaatgcttgtttacaatcattcggtaaaatgtatatcattgccttttttctgataaactaacaaaatcctaatgcagGGAAAACAATTCACGTTCTAAACAAAAATGAGCATGCCTTGGACATGGCTGCTCCAGTGCATGGCAATCCGGGGGATCCAAACGGATCTATGGATGACTA

Basic information

species Zea mays
transcript GRMZM2G157310_T02
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G157310_T02 (Zea mays), 3'ss of exon 6
lower sequence: LOC_Os03g44660.1 (Oryza sativa), 3'ss of exon 6
--actgcacatcattatattaagaagaatgcttgtttacaatcattcggtaaaatgtatatcattgccttttttctgataaactaacaaaatcctaatgcagGGAAAACAATTCACGTTCTAAACAAAAATGAGCATGCCTTGGACATGGCTGCTCCAGTGCATGGCAATCCGGGGGATCCAAACGGATCTATGGATGACTA
  |   ||  |  |   ||| |  |    | || || |   |   ||   |  | |||  | |   ||| |    |||  ||| ||| |     ||||| ||| || || ||||| ||||||||||||||||||||||||||||||||||| ||||||||||||| ||||  ||| |||||||| |||| ||  ||||||||
ctataccatcttttgcaattgatgacttaggttattgattgtttgtctacatcaagtacttaaagacctgtgcattga--aacaaactatggtgtaatgtagGAAAGACTATTCATGTTCTAAACAAAAATGAGCATGCCTTGGACATGGCAGCTCCAGTGCATGACAATTTGGGTGATCCAAATGGATATACTGATGACTA

upper sequence: GRMZM2G157310_T02 (Zea mays), 3'ss of exon 6
lower sequence: AT2G38680.1 (Arabidopsis thaliana), 3'ss of exon 7
-------------------------------------------------------actgcacatcattatattaagaa---gaatgcttgtttacaatcattcggtaa--aatgtatatcattgccttttttctgataaactaacaaaatccta--atgcagGGAAAACAATTCACGTTCTAAACAAAAATGAGCATGCCTTGGACATGGCTGCTCCAGTGCATGGCAATCCGGGGGATCCAAACGGATCTATGGATGACTA
                                                         ||    |  |  | |  | ||    |||   | |    ||  ||   | |    || ||| ||||    || |     |||  ||    |  |   |  || |||| ||   ||||||||| ||||||||||| || || || || ||||||||||||||| | ||||     |  || | |   |  ||       |||||  |
gtataatatttggttggtgtttcatcattcatttaagcgcattcatcaactcacatttgtggtttttcctctggaaaactgaaatctctctcagaaagtatcaagcatttgatttatgtcatgctattataaactatagtctctttacctttcacaatacagGAAAGCTAATTCACGTGCTAAACAAAAACGAACACGCTTTAGACATGGCTGCTCCACTTCATGATCGACTTGGTGTTGACATTGGTGAGGAAGATGAAGA
















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|101386461|gb|EB815247.1|EB815247
EST:     CTCCAACAGGATGGTGTTTAATGAAGAAGGCCGCCTCATAGCATTTAAAG                         GGAAAACAATTCACGTTCTAAACAAAAATG
genomic: CTCCAACAGGATGGTGTTTAATGAAGAAGGCCGCCTCATAGCATTTAAAGgtgattttta ... cctaatgcagGGAAAACAATTCACGTTCTAAACAAAAATG
EST: gi|149013204|gb|EE042840.2|EE042840
EST:     CTCCAACAGGATGGTGTTTAATGAAGAAGGCCGCCTCATAGCATTTAAAG                         GGAAAACAATTCACGTTCTAAACAAAAATGAGCATGCCTTGGACATGGCTG
genomic: CTCCAACAGGATGGTGTTTAATGAAGAAGGCCGCCTCATAGCATTTAAAGgtgattttta ... cctaatgcagGGAAAACAATTCACGTTCTAAACAAAAATGAGCATGCCTTGGACATGGCTG
EST: gi|76293679|gb|DV033247.1|DV033247
EST:     CTCCAACAGGATGGTGTTTAATGAAGAAGGCCGCCTCATAGCATTTAAAG                         GGAAAACAATTCACGTTCTAAACAAAAATGAGCATGCCTTGGACATGGCTG
genomic: CTCCAACAGGATGGTGTTTAATGAAGAAGGCCGCCTCATAGCATTTAAAGgtgattttta ... cctaatgcagGGAAAACAATTCACGTTCTAAACAAAAATGAGCATGCCTTGGACATGGCTG
EST: gi|101385767|gb|EB814932.1|EB814932
EST:     CTCCAACAGGATGGTGTTTAATGAAGAAGGCCGCCTCATAGCATTTAAAG                         GGAAAACAATTCACGTTCTAAACAAAAATGAGCATGCCCTGGACATGGCTG
genomic: CTCCAACAGGATGGTGTTTAATGAAGAAGGCCGCCTCATAGCATTTAAAGgtgattttta ... cctaatgcagGGAAAACAATTCACGTTCTAAACAAAAATGAGCATGCCTTGGACATGGCTG
EST: gi|74242168|gb|DT650082.1|DT650082
EST:     CTCCAACAGGATGGTGTTTAATGAAGAAGGCCGCCTCATAGCATTTAAAG                         GGAAAACAATTCACGTTCTAAACAAAAATGAGCATGCCTTGGACATGGCTG
genomic: CTCCAACAGGATGGTGTTTAATGAAGAAGGCCGCCTCATAGCATTTAAAGgtgattttta ... cctaatgcagGGAAAACAATTCACGTTCTAAACAAAAATGAGCATGCCTTGGACATGGCTG
EST: gi|78092209|gb|DV520583.1|DV520583
EST:     CTCCAACAGGATGGTGTTTAATGAAGAAGGCCGCCTCATAGCATTTAAAG                         GGAAAACAATTCACGTTCTAAACAAAAATGAGCATGCCTTGGACATGGCTG
genomic: CTCCAACAGGATGGTGTTTAATGAAGAAGGCCGCCTCATAGCATTTAAAGgtgattttta ... cctaatgcagGGAAAACAATTCACGTTCTAAACAAAAATGAGCATGCCTTGGACATGGCTG
EST: gi|71774185|gb|DR972065.1|DR972065
EST:     CTCCAACAGGATGGTGTTTAATGAAGAAGGCCGCCTCATAGCATTTAAAG                         GGAAAACAATTCACGTTCTAAACAAAAATGAGCATGCCTTGGACATGGCTG
genomic: CTCCAACAGGATGGTGTTTAATGAAGAAGGCCGCCTCATAGCATTTAAAGgtgattttta ... cctaatgcagGGAAAACAATTCACGTTCTAAACAAAAATGAGCATGCCTTGGACATGGCTG
EST: gi|91877197|gb|EB407154.1|EB407154
EST:     CTCCAACAGGATGGTGTTTAATGAAGAAGGCCGCCTCATAGCATTTAAAG                         GGAAAACAATTCACGTTCTAAACAAAAATGAGCATGCCTTGGACATGGCTG
genomic: CTCCAACAGGATGGTGTTTAATGAAGAAGGCCGCCTCATAGCATTTAAAGgtgattttta ... cctaatgcagGGAAAACAATTCACGTTCTAAACAAAAATGAGCATGCCTTGGACATGGCTG
EST: gi|149009394|gb|EE153935.2|EE153935
EST:     CTCCAACAGGATGGTGTTTAATGAAGAAGGCCGCCTCATAGCATTTAAAG                         GGAAAACAATTCACGTTCTAAACAAAAATGAGCATGCCTTGGACATGGCTG
genomic: CTCCAACAGGATGGTGTTTAATGAAGAAGGCCGCCTCATAGCATTTAAAGgtgattttta ... cctaatgcagGGAAAACAATTCACGTTCTAAACAAAAATGAGCATGCCTTGGACATGGCTG
EST: gi|31354764|gb|CD439121.1|CD439121
EST:     CTCCAACAGGATGGTGTTTAATGAAGAAGGCCGTCTCATAGCATTTAAAG                         GGAAAACAATTCACGTTCTAAACAAAAATGAGCATGCCTTGGACATGGCTG
genomic: CTCCAACAGGATGGTGTTTAATGAAGAAGGCCGCCTCATAGCATTTAAAGgtgattttta ... cctaatgcagGGAAAACAATTCACGTTCTAAACAAAAATGAGCATGCCTTGGACATGGCTG
EST: gi|78092208|gb|DV520582.1|DV520582
EST:     CTCCAACAGGATGGTGTTTAATGAAGAAGGCCGCCTCATAGCATTTAAAG                         GGAAAACAATTCACGTTCTAAACAAAAATGAGCATGCCTTGGACATGGCTG
genomic: CTCCAACAGGATGGTGTTTAATGAAGAAGGCCGCCTCATAGCATTTAAAGgtgattttta ... cctaatgcagGGAAAACAATTCACGTTCTAAACAAAAATGAGCATGCCTTGGACATGGCTG
EST: gi|71438827|gb|DR819877.1|DR819877
EST:     CTCCAACAGGATGGTGTTTAATGAAGAAGGCCGCCTCATAGCATTTAAAG                         GGAAAACAATTCACGTTCTAAACAAAAATGAGCATGCCTTGGACATGGCTG
genomic: CTCCAACAGGATGGTGTTTAATGAAGAAGGCCGCCTCATAGCATTTAAAGgtgattttta ... cctaatgcagGGAAAACAATTCACGTTCTAAACAAAAATGAGCATGCCTTGGACATGGCTG
EST: gi|37400710|gb|CF637712.1|CF637712
EST:     CTCCAACAGGATGGTGTTTAATGAAGAAGGCCGTCTCATAGCATTTAAAG                         GGAAAACAATTCACGTTCTAAACAAAAATGAGCATGCCTTGGACATGGCTG
genomic: CTCCAACAGGATGGTGTTTAATGAAGAAGGCCGCCTCATAGCATTTAAAGgtgattttta ... cctaatgcagGGAAAACAATTCACGTTCTAAACAAAAATGAGCATGCCTTGGACATGGCTG
EST: gi|50333544|gb|CO528670.1|CO528670
EST:     CTCCAACAGGATGGTGTTTAATGAAGAAGGCCGCCTCATAGCATTTAAAG                         GGAAAACAATTCACGTTCTAAACAAAAATGAGCATGCCTTGGACATGGCTG
genomic: CTCCAACAGGATGGTGTTTAATGAAGAAGGCCGCCTCATAGCATTTAAAGgtgattttta ... cctaatgcagGGAAAACAATTCACGTTCTAAACAAAAATGAGCATGCCTTGGACATGGCTG
EST: gi|88749393|gb|DY533534.1|DY533534
EST:     CTCCAACAGGATGGTGTTTAATGAAGAAGGCCGCCTCATAGCATTTAAAG                         GGAAAACAATTCACGTTCTAAACAAAAATGAGCATGCCTTGGACATGGCTG
genomic: CTCCAACAGGATGGTGTTTAATGAAGAAGGCCGCCTCATAGCATTTAAAGgtgattttta ... cctaatgcagGGAAAACAATTCACGTTCTAAACAAAAATGAGCATGCCTTGGACATGGCTG
EST: gi|71449422|gb|DR830472.1|DR830472
EST:     CTCCAACAGGATGGTGTTTAATGAAGAAGGCCGCCTCATAGCATTTAAAG                         GGAAAACAATTCACGTTCTNAACAAAAATGAGCATGCCTTGGACATGGCTG
genomic: CTCCAACAGGATGGTGTTTAATGAAGAAGGCCGCCTCATAGCATTTAAAGgtgattttta ... cctaatgcagGGAAAACAATTCACGTTCTAAACAAAAATGAGCATGCCTTGGACATGGCTG

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: 61

GTCTTCCGGCAGAAATTACACAAAACATTCAAGAACATCAAGGTTGTCTCCAACAGGATGGTGTTTAATGAAGAAGGCCGCCTCATAGCATTTAAAGgtgattttta ... cctaatgcagGGAAAACAATTCACGTTCTAAACAAAAATGAGCATGCCTTGGACATGGCTGCTCCAGTGCATGGCAATCCGGGGGATCCAAACGGATCTATGGATGACTA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 39

GTCTTCCGGCAGAAATTACACAAAACATTCAAGAACATCAAGGTTGTCTCCAACAGGATGGTGTTTAATGAAGAAGGCCGCCTCATAGCATTTAAAGgtgattttta ... cctaatgcagGGAAAACAATTCACGTTCTAAACAAAAATGAGCATGCCTTGGACATGGCTGCTCCAGTGCATGGCAATCCGGGGGATCCAAACGGATCTATGGATGACTA


Block sizes: 43 (upstream exon), 49 (downstream exon)
Score: 30

GTCTTCCGGCAGAAATTACACAAAACATTCAAGAACATCAAGGTTGTCTCCAACAGGATGGTGTTTAATGAAGAAGGCCGCCTCATAGCATTTAAAGgtgattttta ... cctaatgcagGGAAAACAATTCACGTTCTAAACAAAAATGAGCATGCCTTGGACATGGCTGCTCCAGTGCATGGCAATCCGGGGGATCCAAACGGATCTATGGATGACTA


Block sizes: 46 (upstream exon), 49 (downstream exon)
Score: 36

GTCTTCCGGCAGAAATTACACAAAACATTCAAGAACATCAAGGTTGTCTCCAACAGGATGGTGTTTAATGAAGAAGGCCGCCTCATAGCATTTAAAGgtgattttta ... cctaatgcagGGAAAACAATTCACGTTCTAAACAAAAATGAGCATGCCTTGGACATGGCTGCTCCAGTGCATGGCAATCCGGGGGATCCAAACGGATCTATGGATGACTA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ggtaaaatgtatatcattgccttttttctgataaactaacaaaatcctaatgcagGGAAAACAATTCACGTTCTAAACAAAAATGAGCATGCCTTGGACATGGCTGCTCCAGTGCATGGCAATCCGGGGGATCCAAACGGATCTATGGATGACTA
                              ataaactaacaaaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
actgcacatcattatattaagaagaatgcttgtttacaatcattcggtaaaatgtatatcattgccttttttctgataaactaacaaaatcctaatgcagGGAAAACAATTCACGTTCTAAACAAAAATGAGCATGCCTTGGACATGGCTGCTCCAGTGCATGGCAATCCGGGGGATCCAAACGGATCTATGGATGACTA

actgcac
- - - - - - - - - aagaagaa
- - - - - - - - - - - - - tgcttgt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aacaaaa