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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgcatgtcttagctgatgtacagtattaccatgcatgtggtaatttgttcatgtcaacttttgcatgaaattatgtcagGGTTATTGGATGGTTAAGCGTGCTGTAGGAACAAAAGCTTGCCTTCTGGGCAAAGCAGTAACGTGCAATTATCTTCGCCAGGATAACTTTCTGGAG

Basic information

species Zea mays
transcript GRMZM2G160927_T01
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G160927_T01 (Zea mays), 3'ss of exon 7
lower sequence: LOC_Os08g34060.3 (Oryza sativa), 3'ss of exon 19
gtatgcatgtcttagctgatgtacagtattaccatgcatgtgg--taatttgtt----------catgtcaacttttgcatg-------------aaattatgtcagGGTTATTGGATGGTTAAGCGTGCTGTAGGAACAAAAGCTTGCCTTCTGGGCAAAGCAGTAACGTGCAATTATCTTCGCCAGGATAACTTTCTGGAG
||||||||  ||||  | ||||    ||||| | ||||||||   | ||||||            | |||||  |||  |||             |||| || |||||||||||||||||| || ||||| || |||||||||||||| |||||||| ||||||||||| |||||||| |||||||||||||||||||| |||
gtatgcattacttaatttatgtttcttattatcttgcatgtgaattgatttgtgaaactggtgataagtcaaacttttgatgtgaattgaactataaatgatctcagGGTTATTGGATGGTAAAACGTGCAGTTGGAACAAAAGCTTGTCTTCTGGGAAAAGCAGTAACATGCAATTACCTTCGCCAGGATAACTTTCTAGAG

upper sequence: GRMZM2G160927_T01 (Zea mays), 3'ss of exon 7
lower sequence: GLYMA13G22460.1 (Glycine max), 3'ss of exon 19
gtatgcatgtcttagctgatgtacagtat-taccatgcatgtggtaatttgtt---catgtcaacttttg--catgaaattatgtcagGGTTATTGGATGGTTAAGCGTGCTGTAGGAACAAAAGCTTGCCTTCTGGGCAAAGCAGTAACGTGCAATTATCTTCGCCAGGATAACTTTCTGGAG
|| || |  || ||  ||| ||    ||| ||      || || | | |  |      ||||| ||  |     | |||||    ||||| ||||||||||| ||| | ||||||||||| |||||||||||  | || ||||| || || || || ||  || | || ||||| ||| |||||
gtgtg-agatcctaaatgaagtgttatatatatgccctatttgatgactgatagcatttgtcagctaatagttttcaaattgatacagGGATATTGGATGGTCAAGAGAGCTGTAGGAACCAAAGCTTGCCTCTTAGGAAAAGCTGTGACTTGTAAATACTTTAGACAAGATAATTTTTTGGAG

upper sequence: GRMZM2G160927_T01 (Zea mays), 3'ss of exon 7
lower sequence: GLYMA17G11250.1 (Glycine max), 3'ss of exon 19
gtatgcatgtcttagctgatgtacagtat-taccatgcatg-tggtaatttgttcatgtcaactttt-gcatgaaattatgtcagGGTTATTGGATGGTTAAGCGTGCTGTAGGAACAAAAGCTTGCCTTCTGGGCAAAGCAGTAACGTGCAATTATCTTCGCCAGGATAACTTTCTGGAG
|| ||    || |   ||| ||    ||| | || |   || ||     | |    |||||  |  | |  |  ||||    ||||| ||||||||||| ||| | ||||||||||| |||||||||||  | || ||||| || || || || ||  || | || ||||| ||| |||||
gtgtgtg-atcctcaatgaagtgttatatatgccctatttgatgactgatagcatttgtcagttgatagttttcaattgatacagGGATATTGGATGGTCAAGAGAGCTGTAGGAACCAAAGCTTGCCTCTTAGGAAAAGCTGTGACTTGTAAATACTTTAGACAAGATAATTTTTTGGAG

upper sequence: GRMZM2G160927_T01 (Zea mays), 3'ss of exon 7
lower sequence: GLYMA15G26120.1 (Glycine max), 3'ss of exon 7
--gtatgcatgtcttagctgat--gtacagtattaccatgcatgtggtaatttgttcatgtcaacttttgcatgaaattatgtcagGGTTATTGGATGGTTAAGCGTGCTGTAGGAACAAAAGCTTGCCTTCTGGGCAAAGCAGTAACGTGCAATTATCTTCGCCAGGATAACTTTCTGGAG
  || ||  | | | || ||||   ||     ||   ||  || | |||     || | |  | |  | |  |  ||       |||| ||||||||||| ||||| ||||||||||||||||||||||| || || ||||| || || || || ||  ||   || ||||| ||| | |||
gtgtgtgattctttaagatgattcatatgccttttttatttattttgtatagcattga-gcaaccaatggttttcaacggatgtagGGATATTGGATGGTCAAGCGAGCTGTAGGAACAAAAGCTTGCCTACTAGGGAAAGCTGTCACTTGTAAATACTTTAAACAAGATAATTTTTTTGAG

upper sequence: GRMZM2G160927_T01 (Zea mays), 3'ss of exon 7
lower sequence: AT5G35180.4 (Arabidopsis thaliana), 3'ss of exon 22
gtatgcatgtcttagctgatgtacagtattaccatgcatgtggtaa-tttgttcatgtc--aacttttgcatgaaattatgtcagGGTTATTGGATGGTTAAGCGTGCTGTAGGAACAAAAGCTTGCCTTCTGGGCAAAGCAGTAACGTGCAATTATCTTCGCCAGGATAACTTTCTGGAG
|||   |   ||  |||  | | |  |   ||     || | ||||  ||  |||  |   |||  |       ||| |   ||||| ||||||||||| ||||| ||||| ||||||||||| ||| | || || ||||| || || || || || ||  | |||||||||||| |||||
gtaaaga-aactctgctcttct-cgtttccactg-aaatatagtaaacttagtcacattgtaaccgtcatggtgaatca---cagGGATATTGGATGGTCAAGCGGGCTGTTGGAACAAAAGCCTGCTTGCTCGGTAAAGCTGTGACCTGTAAGTACCTGAGGCAGGATAACTTTTTGGAG

upper sequence: GRMZM2G160927_T01 (Zea mays), 3'ss of exon 7
lower sequence: PP1S91_96V6.1 (Physcomitrella patens), 3'ss of exon 20
--------gta-tgcatgtcttagctgat---gtacagtattaccatgcatgtggtaatttgttca-tgtcaa--cttttgcatgaaattatgtc---agGGTTATTGGATGGTTAAGCGTGCTGTAGGAACAAAAGCTTGCCTTCTGGGCAAAGCAGTAACGTGCAATTATCTTCGCCAGGATAACTTTCTGGAG
         |  ||| |||| |  ||  |   ||    ||   |  |   |    ||||  || || ||||||     |  | |    ||   ||   ||||||| |||||||| || |||||||| || ||||||||||| || ||||| ||||| || || ||||||||  | ||  | || || || || |||
tgttcacaatgctgcttgtcctgcctcttctggtttcatacaccgttaagttctataatgcgtgcagtgtcaaggtcctaacgttccgtttcttctccagGGTTACTGGATGGTGAAACGTGCTGTTGGTACAAAAGCTTGTCTGCTGGGTAAAGCTGTTACTTGCAATTACTTGCGTAAAGACAATTTCCTTGAG

upper sequence: GRMZM2G160927_T01 (Zea mays), 3'ss of exon 7
lower sequence: PP1S376_46V6.1 (Physcomitrella patens), 3'ss of exon 18
------gtatg-catgtcttagctgatgtacagtattaccatgcat--gtggta---atttgttcatg--tcaacttttg-catgaaatta---tgtcagGGTTATTGGATGGTTAAGCGTGCTGTAGGAACAAAAGCTTGCCTTCTGGGCAAAGCAGTAACGTGCAATTATCTTCGCCAGGATAACTTTCTGGAG
       |||| || || | |     | | |  | | |  | | ||  ||  ||   | |   |  ||  |||  || |  ||| | |||    | | |||||||||||||||| ||||||||||| || |||||||| ||||| ||||||||||| || || || |||||  | ||    ||||| ||||| |||
tgtttattatggcacgtttgattatgttttctctttcaagacgaataggtaatacctactgccttgtgaatcagtttctaacattacattgatttcttagGGTTATTGGATGGTGAAGCGTGCTGTTGGTACAAAAGCATGCCTACTGGGCAAAGCTGTCACTTGTAATTACTTGCGTAGAGATAATTTTCTTGAG

upper sequence: GRMZM2G160927_T01 (Zea mays), 3'ss of exon 7
lower sequence: PP1S141_3V6.1 (Physcomitrella patens), 3'ss of exon 18
-------gtatgcatgtcttagctgatgtacagtattaccatgcatg--tggta-atttgttcatgtcaacttttgcatgaaattatgt--------cagGGTTATTGGATGGTTAAGCGTGCTGTAGGAACAAAAGCTTGCCTTCTGGGCAAAGCAGTAACGTGCAATTATCTTCGCCAGGATAACTTTCTGGAG
       | | |    | | |  | ||||    | |    ||| |||  || |  ||    |  ||  ||  ||| |   | |    ||        |||||||| |||||||| ||||||||||| || |||||||| || || ||||| || || || || || |||||  | ||| | |||||||| || |||
tttttttgaaagacaatgtgattttatgttttttttcgagatggatgcatgatgcatacactgttgggaatcttttctcaacacctcgttcaatccacagGGTTACTGGATGGTGAAGCGTGCTGTTGGTACAAAAGCCTGTCTACTGGGTAATGCTGTCACTTGTAATTACTTGCGCAAAGATAACTTCCTTGAG

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|60397419|gb|DN230235.1|DN230235
EST:     CTGATGCATACCGAGATGCCAGATTTAAACTTATACCAAGCATTGTTGAG                         GGTTATTGGATGGTTAAGCGTGCTGTAGGAACAAAAGCTTGCCTTCTGGGC
genomic: CTGATGCATACCGAGATGCCAGATTTAAACTTATACCAAGCATTGTTGAGgtatgcatgt ... attatgtcagGGTTATTGGATGGTTAAGCGTGCTGTAGGAACAAAAGCTTGCCTTCTGGGC
EST: gi|211510092|gb|FL332408.1|FL332408
EST:     CTGATGCATACCGAGATGCCAGATTTAAACTTATACCAAGCATTGTTGAG                         GGTTATTGGATGGTTAAGCGTGCTGTAGGAACAAAAGCTTGCCTTCTGGGT
genomic: CTGATGCATACCGAGATGCCAGATTTAAACTTATACCAAGCATTGTTGAGgtatgcatgt ... attatgtcagGGTTATTGGATGGTTAAGCGTGCTGTAGGAACAAAAGCTTGCCTTCTGGGC
EST: gi|32839402|gb|CD979083.1|CD979083
EST:     CTGATGCATACCGAGATGCCAGATTTAAACTTATACCAAGCATTGTTGAG                         GGTTATTGGATGGTTAAGCGTGCTGTAGGAACAAAAGCTTGCCTTCTGGGC
genomic: CTGATGCATACCGAGATGCCAGATTTAAACTTATACCAAGCATTGTTGAGgtatgcatgt ... attatgtcagGGTTATTGGATGGTTAAGCGTGCTGTAGGAACAAAAGCTTGCCTTCTGGGC
EST: gi|37394737|gb|CF634645.1|CF634645
EST:     CTGATGCATACCGAGATGCCAGATTTAAACTTATACCAAGCATTGTTGAG                         GGTTATTGGATGGTTAAGCGTGCTGTAGGAACAAAAGCTTGCCTTCTGGGC
genomic: CTGATGCATACCGAGATGCCAGATTTAAACTTATACCAAGCATTGTTGAGgtatgcatgt ... attatgtcagGGTTATTGGATGGTTAAGCGTGCTGTAGGAACAAAAGCTTGCCTTCTGGGC
EST: gi|32837394|gb|CD977072.1|CD977072
EST:     CTGATGCATACCGAGATGCCAGATTTAAACTTATACCAAGCATTGTTGAG                         GGTTATTGGATGGTTAAGCGTGCTGTAGGAACAAAAGCTTGCCTTCTGGGC
genomic: CTGATGCATACCGAGATGCCAGATTTAAACTTATACCAAGCATTGTTGAGgtatgcatgt ... attatgtcagGGTTATTGGATGGTTAAGCGTGCTGTAGGAACAAAAGCTTGCCTTCTGGGC
EST: gi|71439002|gb|DR820052.1|DR820052
EST:     CTGATGCATACCGAGATGCCAGATTTAAACTTATACCAAGCATTGTTGAG                         GGTTATTGGATGGTTAAGCGTGCTGTAGGAACAAAAGCTTGCCTTCTGGGC
genomic: CTGATGCATACCGAGATGCCAGATTTAAACTTATACCAAGCATTGTTGAGgtatgcatgt ... attatgtcagGGTTATTGGATGGTTAAGCGTGCTGTAGGAACAAAAGCTTGCCTTCTGGGC
EST: gi|211119644|gb|FL444181.1|FL444181
EST:     CTGATGCATACCGAGATGCCAGATTTAAACTTATACCAAGCATTGTTGAG                         GGTTATTGGATGGTTAAGCGTGCTGTAGGAACAAAAGCTTGCCTTYTGGGT
genomic: CTGATGCATACCGAGATGCCAGATTTAAACTTATACCAAGCATTGTTGAGgtatgcatgt ... attatgtcagGGTTATTGGATGGTTAAGCGTGCTGTAGGAACAAAAGCTTGCCTTCTGGGC
EST: gi|60338548|gb|DN205521.1|DN205521
EST:     CTGATGCATACCGAGATGCCAGATTTAAACTTATACCAAGCATTGTTGAG                         GGTTATTGGATGGTTAAGCGTGCTGTAGGAACAAAAGCTTGCCTTCTGGGC
genomic: CTGATGCATACCGAGATGCCAGATTTAAACTTATACCAAGCATTGTTGAGgtatgcatgt ... attatgtcagGGTTATTGGATGGTTAAGCGTGCTGTAGGAACAAAAGCTTGCCTTCTGGGC
EST: gi|211043352|gb|FL434187.1|FL434187
EST:     CTGATGCATACCGAGATGCCAGATTTAAACTTATACCAAGCATTGTTGAG                         GGTTATTGGATGGTTAAGCGTGCTGTAGGAACAAAAGCTTGCCTTCTGGGC
genomic: CTGATGCATACCGAGATGCCAGATTTAAACTTATACCAAGCATTGTTGAGgtatgcatgt ... attatgtcagGGTTATTGGATGGTTAAGCGTGCTGTAGGAACAAAAGCTTGCCTTCTGGGC
EST: gi|5901061|gb|AW042161.1|AW042161
EST:     CTGATGCATACCGAGATGCCAGATTTAAACTTATACCAAGCATTGTTGAG                         GGTTATTGGATGGTTAAGCGTGCTGTAGGAACAAAAGCTTGCCTTCTGGGC
genomic: CTGATGCATACCGAGATGCCAGATTTAAACTTATACCAAGCATTGTTGAGgtatgcatgt ... attatgtcagGGTTATTGGATGGTTAAGCGTGCTGTAGGAACAAAAGCTTGCCTTCTGGGC
EST: gi|211488642|gb|FL313368.1|FL313368
EST:     CTGATGCATACCGAGATGCCAGATTTAAACTTATACCAAGCATTGTTGAG                         GGTTATTGGATGGTTAAGCGTGCTGTAGGAACAAAAGCTTGCCTTMTGGGC
genomic: CTGATGCATACCGAGATGCCAGATTTAAACTTATACCAAGCATTGTTGAGgtatgcatgt ... attatgtcagGGTTATTGGATGGTTAAGCGTGCTGTAGGAACAAAAGCTTGCCTTCTGGGC
EST: gi|33942624|gb|CF349224.1|CF349224
EST:     CTGATGCATACCGAGATGCCAGATTTAAACTTATACCAAGCATTGTTGAG                         GGTTATTGGATGGTTAAGCGTGCTGTAGGAACAAAAGCTTGCCTTCTGGGC
genomic: CTGATGCATACCGAGATGCCAGATTTAAACTTATACCAAGCATTGTTGAGgtatgcatgt ... attatgtcagGGTTATTGGATGGTTAAGCGTGCTGTAGGAACAAAAGCTTGCCTTCTGGGC
EST: gi|94476383|gb|EB705341.1|EB705341
EST:     CTGATGCATACCGAGATGCCAGATTTAAACTTATACCAAGCATTGTTGAG                         GGTTATTGGATGGTTAAGCGTGCTGTAGGAACAAAAGCTTGCCTTCTGGGC
genomic: CTGATGCATACCGAGATGCCAGATTTAAACTTATACCAAGCATTGTTGAGgtatgcatgt ... attatgtcagGGTTATTGGATGGTTAAGCGTGCTGTAGGAACAAAAGCTTGCCTTCTGGGC
EST: gi|32935302|gb|CF040114.1|CF040114
EST:     CTGATGCATACCGAGATGCCAGATTTAAACTTATACCAAGCATTGTTGAG                         GGTTATTGGATGGTTAAGCGTGCTGTAGGAACAAAAGCTTGCCTTCTGGGC
genomic: CTGATGCATACCGAGATGCCAGATTTAAACTTATACCAAGCATTGTTGAGgtatgcatgt ... attatgtcagGGTTATTGGATGGTTAAGCGTGCTGTAGGAACAAAAGCTTGCCTTCTGGGC
EST: gi|32837391|gb|CD977069.1|CD977069
EST:     CTGATGCATACCGAGATGCCAGATTTAAACTTATACCAAGCATTGTTGAG                         GGTTATTGGATGGTTAAGCGTGCTGTAGGAACAAAAGCTTGCCTTCTGGGC
genomic: CTGATGCATACCGAGATGCCAGATTTAAACTTATACCAAGCATTGTTGAGgtatgcatgt ... attatgtcagGGTTATTGGATGGTTAAGCGTGCTGTAGGAACAAAAGCTTGCCTTCTGGGC

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: 46 (upstream exon), 47 (downstream exon)
Score: 171

AGAGAGACCAGTGAACAAAGATTCTTTGTTGGGTAGATTCATTGATGGAACTGATGCATACCGAGATGCCAGATTTAAACTTATACCAAGCATTGTTGAGgtatgcatgt ... attatgtcagGGTTATTGGATGGTTAAGCGTGCTGTAGGAACAAAAGCTTGCCTTCTGGGCAAAGCAGTAACGTGCAATTATCTTCGCCAGGATAACTTTCTGGAG


Block sizes: 46 (upstream exon), 48 (downstream exon)
Score: 68

AGAGAGACCAGTGAACAAAGATTCTTTGTTGGGTAGATTCATTGATGGAACTGATGCATACCGAGATGCCAGATTTAAACTTATACCAAGCATTGTTGAGgtatgcatgt ... attatgtcagGGTTATTGGATGGTTAAGCGTGCTGTAGGAACAAAAGCTTGCCTTCTGGGCAAAGCAGTAACGTGCAATTATCTTCGCCAGGATAACTTTCTGGAG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 116

AGAGAGACCAGTGAACAAAGATTCTTTGTTGGGTAGATTCATTGATGGAACTGATGCATACCGAGATGCCAGATTTAAACTTATACCAAGCATTGTTGAGgtatgcatgt ... attatgtcagGGTTATTGGATGGTTAAGCGTGCTGTAGGAACAAAAGCTTGCCTTCTGGGCAAAGCAGTAACGTGCAATTATCTTCGCCAGGATAACTTTCTGGAG


Block sizes: 47 (upstream exon), 45 (downstream exon)
Score: 123

AGAGAGACCAGTGAACAAAGATTCTTTGTTGGGTAGATTCATTGATGGAACTGATGCATACCGAGATGCCAGATTTAAACTTATACCAAGCATTGTTGAGgtatgcatgt ... attatgtcagGGTTATTGGATGGTTAAGCGTGCTGTAGGAACAAAAGCTTGCCTTCTGGGCAAAGCAGTAACGTGCAATTATCTTCGCCAGGATAACTTTCTGGAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

attaccatgcatgtggtaatttgttcatgtcaacttttgcatgaaattatgtcagGGTTATTGGATGGTTAAGCGTGCTGTAGGAACAAAAGCTTGCCTTCTGGGCAAAGCAGTAACGTGCAATTATCTTCGCCAGGATAACTTTCTGGAG
                                        atgaaattat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgcatgtcttagctgatgtacagtattaccatgcatgtggtaatttgttcatgtcaacttttgcatgaaattatgtcagGGTTATTGGATGGTTAAGCGTGCTGTAGGAACAAAAGCTTGCCTTCTGGGCAAAGCAGTAACGTGCAATTATCTTCGCCAGGATAACTTTCTGGAG

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