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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tttcttatgatatcctgtgcaccatattttcttctggagtatgttagaaacaaaacaattctgcagttttctttaacatatggatttggcaaatctgcagGTTGAACATGTAATTAGGGAACAGAACTTTATGGCAGCCAACGAGATCATTGAGCTCTTCTGCGAGCTGATTGTTACACGCCTTCCTATCATCGCAAAAC

Basic information

species Zea mays
transcript GRMZM2G012413_T01
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G012413_T01 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os09g37510.1 (Oryza sativa), 3'ss of exon 2
tttcttatgatatcctgtgcaccatattttcttctggagtatgttagaaacaaaacaattctg--cagttttctttaacatatggatttggcaaatctgcagGTTGAACATGTAATTAGGGAACAGAACTTTATGGCAGCCAACGAGATCATTGAGCTCTTCTGCGAGCTGATTGTTACACGCCTTCCTATCATCGCAAAAC
 | |  ||   |   ||||||   |||||  |    ||  |    | |  |  |   || |||  ||  |||||     |  |   |||||    | | |||||||| ||||| ||||| ||||||||| |||||||||| || ||||||||||| || ||||| ||||||||||||||||||||||| ||||| ||||| |
-tgcagattggaatatgtgcatggtatttcttgagtgaaaaaacaacatgctta-tgatgctgatcatatttctcatgaagctatttttgggctttttacagGTTGAGCATGTCATTAGAGAACAGAACATTATGGCAGCGAATGAGATCATTGATCTTTTCTGTGAGCTGATTGTTACACGCCTTCCCATCATTGCAAAGC

upper sequence: GRMZM2G012413_T01 (Zea mays), 3'ss of exon 2
lower sequence: AT4G35730.1 (Arabidopsis thaliana), 3'ss of exon 2
tttcttatgatatcctgtgcaccatattttcttc--tggagtatgttagaaacaaaacaattctgcagttttctttaacatatggatttggcaaatctgcagGTTGAACATGTAATTAGGGAACAGAACTTTATGGCAGCCAACGAGATCATTGAGCTCTTCTGCGAGCTGATTGTTACACGCCTTCCTATCATCGCAAAAC
          |||        ||   ||  |||   | |||| |       |     ||||||        | ||   | | |   |||| ||||| |  ||||||| ||||| || |||||||||||| ||  |||||| ||||| ||||||||||| ||||| || || |||||| | || ||  |||||||| | || |
---------gtatttcactttcctggttcactttgttagagttttccctggatcgttcaattcaatgaagatttt--gctttt---tttgacaaattt--agGTTGAGCATGTGATAAGGGAACAGAACATTCAGGCAGCAAACGAAATCATTGAGCTTTTCTGTGAACTTATTGTTTCTCGTCTCACTATCATCACTAAGC
















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|74241634|gb|DT649548.1|DT649548
EST:     ACATTGCCGCGCTCCTCCGCGACAAACAGGAGGATACCGCACGCATCAGG                         GTTGAACATGTAATTAGGGAACAGAACTTTATGGCAGCCAACGAGATCATT
genomic: ACATTGCCGCGCTCCTCCGCGACAAACAGGAGGATACCGCACGCATCAGGgtaagcactc ... aaatctgcagGTTGAACATGTAATTAGGGAACAGAACTTTATGGCAGCCAACGAGATCATT
EST: gi|148999901|gb|EE036946.2|EE036946
EST:     ACATTGCCGCGCTCCTCCGCGACAAACAGGAGGATACCGCACGCATCAGG                         GTTGAACATGTAATTAGGGAACAGAACTTTATGGCAGCCAACGAGATCATT
genomic: ACATTGCCGCGCTCCTCCGCGACAAACAGGAGGATACCGCACGCATCAGGgtaagcactc ... aaatctgcagGTTGAACATGTAATTAGGGAACAGAACTTTATGGCAGCCAACGAGATCATT
EST: gi|149076185|gb|EE164779.2|EE164779
EST:     ACATTGCCGCGCTCCTCCGCGACAAACAGGAGGATACCGCACGCATCAGG                         GTTGAACATGTAATTAGGGAACAGAACTTTATGGCAGCCAACGAGATCATT
genomic: ACATTGCCGCGCTCCTCCGCGACAAACAGGAGGATACCGCACGCATCAGGgtaagcactc ... aaatctgcagGTTGAACATGTAATTAGGGAACAGAACTTTATGGCAGCCAACGAGATCATT
EST: gi|211434274|gb|FL405875.1|FL405875
EST:     ACATTGCCGCGCTCCTCCGCGACAAACAGGAGGATACCGCACGCATCAGG                         GTTGAACATGTAATTAGGGAACAGAACTTTATGGCAGCCAACGAGATCATT
genomic: ACATTGCCGCGCTCCTCCGCGACAAACAGGAGGATACCGCACGCATCAGGgtaagcactc ... aaatctgcagGTTGAACATGTAATTAGGGAACAGAACTTTATGGCAGCCAACGAGATCATT
EST: gi|148945139|gb|EC890337.2|EC890337
EST:     ACATTGCCGCGCTCCTCCGCGACAAACAGGAGGATACCGCACGCATCAGG                         GTTGAACATGTAATTAGGGAACAGAACTTTATGGCAGCCAACGAGATCATT
genomic: ACATTGCCGCGCTCCTCCGCGACAAACAGGAGGATACCGCACGCATCAGGgtaagcactc ... aaatctgcagGTTGAACATGTAATTAGGGAACAGAACTTTATGGCAGCCAACGAGATCATT
EST: gi|20802742|gb|BQ293792.1|BQ293792
EST:     ACATTGCCGCGCTCCTCCGCGACAAACAGGAGGATACCGCACGCATCAGG                         GTTGAACATGTAATTAGGGAACAGAACTTTATGGCAGCCAACGAGATCATT
genomic: ACATTGCCGCGCTCCTCCGCGACAAACAGGAGGATACCGCACGCATCAGGgtaagcactc ... aaatctgcagGTTGAACATGTAATTAGGGAACAGAACTTTATGGCAGCCAACGAGATCATT
EST: gi|78111386|gb|DV529783.1|DV529783
EST:     ACATTGCCGCGCTCCTCCGCGACAAACAGGAGGATACCGCACGCATCAGG                         GTTGAACATGTAATTAGGGAACAGAACTTTATGGCAGCCAACGAGATCATT
genomic: ACATTGCCGCGCTCCTCCGCGACAAACAGGAGGATACCGCACGCATCAGGgtaagcactc ... aaatctgcagGTTGAACATGTAATTAGGGAACAGAACTTTATGGCAGCCAACGAGATCATT
EST: gi|71322908|gb|DR798137.1|DR798137
EST:     ACATTGCCGCGCTCCTCCGCGACAAACAGGAGGATACCGCACGCATCAGG                         GTTGAACATGTAATTAGGGAACAGAACTTTATGGCAGCCAACGAGATCATT
genomic: ACATTGCCGCGCTCCTCCGCGACAAACAGGAGGATACCGCACGCATCAGGgtaagcactc ... aaatctgcagGTTGAACATGTAATTAGGGAACAGAACTTTATGGCAGCCAACGAGATCATT
EST: gi|71767968|gb|DR965905.1|DR965905
EST:     ACATTGCCGCGCTCCTCCGCGACAAACAGGAGGATACCGCACGCATCAGG                         GTTGAACATGTAATTAGGGAACAGAACTTTATGGCAGCCAACGAGATCATT
genomic: ACATTGCCGCGCTCCTCCGCGACAAACAGGAGGATACCGCACGCATCAGGgtaagcactc ... aaatctgcagGTTGAACATGTAATTAGGGAACAGAACTTTATGGCAGCCAACGAGATCATT
EST: gi|86466457|gb|DY232827.1|DY232827
EST:     ACTTTGCCGCGCTCCTCCGCGACAAACAGGAGGATACCGCACGCATCGGG                         GTTGAACATGTATTTAGGGAACAGAACTTTATGGCAGCCAACGAGATCTTT
genomic: ACATTGCCGCGCTCCTCCGCGACAAACAGGAGGATACCGCACGCATCAGGgtaagcactc ... aaatctgcagGTTGAACATGTAATTAGGGAACAGAACTTTATGGCAGCCAACGAGATCATT
EST: gi|28910124|gb|CB331273.1|CB331273
EST:     ACATTGCCGCGCTCCTCCGCGACAAACAGGAGGATACCGCACGCATCAGG                         GTTGAACATGTAATTAGGGAACAGAACTTTATGGCAGCCAACGAGATCATT
genomic: ACATTGCCGCGCTCCTCCGCGACAAACAGGAGGATACCGCACGCATCAGGgtaagcactc ... aaatctgcagGTTGAACATGTAATTAGGGAACAGAACTTTATGGCAGCCAACGAGATCATT

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: 118

GAAGCTGCTGCGGAACCGGAGGGAGGCGCAGGTGCGCCAGATGCGCCGCGACATTGCCGCGCTCCTCCGCGACAAACAGGAGGATACCGCACGCATCAGGgtaagcactc ... aaatctgcagGTTGAACATGTAATTAGGGAACAGAACTTTATGGCAGCCAACGAGATCATTGAGCTCTTCTGCGAGCTGATTGTTACACGCCTTCCTATCATCGCAAAAC


Block sizes: 46 (upstream exon), 39 (downstream exon)
Score: 11

GAAGCTGCTGCGGAACCGGAGGGAGGCGCAGGTGCGCCAGATGCGCCGCGACATTGCCGCGCTCCTCCGCGACAAACAGGAGGATACCGCACGCATCAGGgtaagcactc ... aaatctgcagGTTGAACATGTAATTAGGGAACAGAACTTTATGGCAGCCAACGAGATCATTGAGCTCTTCTGCGAGCTGATTGTTACACGCCTTCCTATCATCGCAAAAC


Block sizes: 49 (upstream exon), 37 (downstream exon)
Score: 11

GAAGCTGCTGCGGAACCGGAGGGAGGCGCAGGTGCGCCAGATGCGCCGCGACATTGCCGCGCTCCTCCGCGACAAACAGGAGGATACCGCACGCATCAGGgtaagcactc ... aaatctgcagGTTGAACATGTAATTAGGGAACAGAACTTTATGGCAGCCAACGAGATCATTGAGCTCTTCTGCGAGCTGATTGTTACACGCCTTCCTATCATCGCAAAAC


Block sizes: 49 (upstream exon), 44 (downstream exon)
Score: 36

GAAGCTGCTGCGGAACCGGAGGGAGGCGCAGGTGCGCCAGATGCGCCGCGACATTGCCGCGCTCCTCCGCGACAAACAGGAGGATACCGCACGCATCAGGgtaagcactc ... aaatctgcagGTTGAACATGTAATTAGGGAACAGAACTTTATGGCAGCCAACGAGATCATTGAGCTCTTCTGCGAGCTGATTGTTACACGCCTTCCTATCATCGCAAAAC




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agaaacaaaacaattctgcagttttctttaacatatggatttggcaaatctgcagGTTGAACATGTAATTAGGGAACAGAACTTTATGGCAGCCAACGAGATCATTGAGCTCTTCTGCGAGCTGATTGTTACACGCCTTCCTATCATCGCAAAAC
                         ctttaac  putative branch site (score: 36)
                     ttttctttaacatat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tttcttatgatatcctgtgcaccatattttcttctggagtatgttagaaacaaaacaattctgcagttttctttaacatatggatttggcaaatctgcagGTTGAACATGTAATTAGGGAACAGAACTTTATGGCAGCCAACGAGATCATTGAGCTCTTCTGCGAGCTGATTGTTACACGCCTTCCTATCATCGCAAAAC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGAT
- - - - - - - - gtgcacc
- - - - - - - - - - - - - - - cttctgg
- - - - - - - - - - - - - - - - - - - - - - - -aaacaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tctgcag