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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gcagatgttcattccatgattttctaaaccccatataaagctagaaacagttctttaattggaggatcacctttgatctctatgccttttcttgtggcagGTGTTTATGTCATGATGTCAGGGCTTGATCTGGAAAGGCTTGTATTAGCTGCGGGCCCTATTGGCCTTATGCAGGCATGCCTTGATGTTGTACTTCCATA

Basic information

species Zea mays
transcript GRMZM2G381051_T04
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G381051_T01 (Zea mays), 3'ss of exon 8
lower sequence: LOC_Os05g03480.4 (Oryza sativa), 3'ss of exon 9
-----------------------------------------------------------------------------gcagatgtt--cattccatgattttctaaaccccatata-aagctagaaacagttct-----ttaattggaggatcacctttgatctctatgc----cttttcttgtggcagGTGTTTATGTCATGATGTCAGGGCTTGATCTGGAAAGGCTTGTATTAGCTGCGGGCCCTATTGGCCTTATGCAGGCATGCCTTGATGTTGTACTTCCATA
                                                                              ||| ||||  |||      |  | | |     || | | ||    |  | | ||||     || ||      |||| | |  |    |   |     ||||||||| ||||||||||||||||||||||||||||||||||| ||||| ||||| |||||||| || ||||| ||||| ||||| |||||||||||||| |   |||| ||
gtattaactgctgattgtcgtaaacttagtcagaattcttgttgctatcctgagatatttattcagttgtgtacagtacagttgtttgcatctaccaaactgccactgtacacacagaaaactgtcataattctagccattgatcctgttatcatcctcaaagagtgaacagtttttttcttgttgcagGTGTTTATGTCATGATGTCAGGGCTTGATCTAGAAAGACTTGTGTTAGCTGCAGGTCCTATCGGCCTCATGCAAGCATGCCTTGATGTAGCTGTTCCTTA

upper sequence: GRMZM2G381051_T01 (Zea mays), 3'ss of exon 8
lower sequence: GLYMA12G07570.1 (Glycine max), 3'ss of exon 10
gcagatgttcattccatgattttcta---aaccccatataaagctagaaacagttcttta--attggagg---atcacctttgatctctatgccttttcttgtggcagGTGTTTATGTCATGATGTCAGGGCTTGATCTGGAAAGGCTTGTATTAGCTGCGGGCCCTATTGGCCTTATGCAGGCATGCCTTGATGTTGTACTTCCATA
        || || |    ||||| |   ||   |  ||||||  |   ||| ||  |||   ||| | |   |    | || ||  | |    || | ||||  |||| || |||||||||||||| ||||| |||||||| || ||||| || || || || ||| ||||  ||||||||||||| ||||||||||| ||||| ||
--------tcctttctcttttttccatgcaaatactgataaagagaaggacattttgttattgttgcatgtcaagtgtcatttattaccacttattcttttgtttcagGAGTCTATGTCATGATGTCTGGGCTGGATCTGGAGAGACTTGTTTTGGCAGCTGGTCCTCTTGGTATTATGCAGGCATGTCTTGATGTTGTCCTTCCTTA

upper sequence: GRMZM2G381051_T01 (Zea mays), 3'ss of exon 8
lower sequence: GLYMA11G15900.1 (Glycine max), 3'ss of exon 10
gcagatgttcattccatgattttctaaaccccatataaagctagaaacagttcttta--attggaggatcacctttgatctctatgccttttcttgtgg---cagGTGTTTATGTCATGATGTCAGGGCTTGATCTGGAAAGGCTTGTATTAGCTGCGGGCCCTATTGGCCTTATGCAGGCATGCCTTGATGTTGTACTTCCATA
       |||  |   |    | | || ||  ||  ||||  |  |||| ||  |||   ||| | |   |   |   ||  |||  ||| |  | |||   |||| || |||||||||||||| ||||| |||||||| || ||||| || || || || ||| ||||  ||||||||||||| |||||||| || ||||| ||
-----ctttctcttttttcaatgcaaatcctgattaaaagggaagaacatttagttattgttgcatgtcaagtgtcattcattatcacttattctttggtttcagGAGTCTATGTCATGATGTCTGGGCTGGATCTGGAGAGACTTGTTTTGGCAGCTGGTCCTCTTGGTATTATGCAGGCATGTCTTGATGTCGTCCTTCCTTA

upper sequence: GRMZM2G381051_T01 (Zea mays), 3'ss of exon 8
lower sequence: Vv06s0004g03140.t01 (Vitis vinifera), 3'ss of exon 10
gcagatgttcattccatgattttctaaaccccatataaagctagaaacagttctttaattggaggatcacct----ttgatctctatgccttttcttgtggcagGTGTTTATGTCATGATGTCAGGGCTTGATCTGGAAAGGCTTGTATTAGCTGCGGGCCCTATTGGCCTTATGCAGGCATGCCTTGATGTTGTACTTCCATA
       || ||  || | || | | |     || ||    || |   | ||||||  ||      ||  ||    ||||  |   || | ||| |  |  |||| ||||| || |||||||||||||| ||| ||||||||||||| || || || || ||  |||| ||||||||||||||  | ||||| || ||||| ||
-tgagcatttatcaca-gcttatatgattgtaatttatta-taaatgaacttcttttcttttttcttcttctaatattgacattgttgtcctttttcttt-cagGAGTTTACGTAATGATGTCAGGGCTAGATTTGGAAAGGCTTGTTTTGGCAGCTGGGCCCCTTGGTCTTATGCAGGCATGTATAGATGTAGTTCTTCCCTA

upper sequence: GRMZM2G381051_T01 (Zea mays), 3'ss of exon 8
lower sequence: EFJ09244 (Selaginella moellendorffii), 3'ss of exon 11
gcagatgttcattccatgattttctaaaccccatataaagctagaaacagttctttaattggaggatcacctttgatctctatgccttttcttgtggcagGTGTTTATGTCATGATGTCAGGGCTTGATCTGGAAAGGCTTGTATTAGCTGCGGGCCCTATTGGCCTTATGCAGGCATGCCTTGATGTTGTACTTCCATA
                                                  ||  |   ||  | |||     ||| |        | | ||      ||||||||||||| |||||||| ||||| ||| |||| ||||||||||| ||  | || ||| | || || ||||| || ||| | || || || ||||| ||
--------------------------------------------gtgagtttgctgggtttcaagattgaacttgttactagcagcgtatc----aacagGTGTTTATGTGATGATGTCTGGGCTGGATTTGGAGAGGCTTGTATTGGCATCTGGTCCTTTGGGTCTCATGCAAGCTTGCATGGACGTGGTTCTTCCCTA

upper sequence: GRMZM2G381051_T01 (Zea mays), 3'ss of exon 8
lower sequence: EFJ07135 (Selaginella moellendorffii), 3'ss of exon 11
gcagatgttcattccatgattttctaaaccccatataaagctagaaacagttctttaattggaggatcacctttgatctctatgccttttcttgtggcagGTGTTTATGTCATGATGTCAGGGCTTGATCTGGAAAGGCTTGTATTAGCTGCGGGCCCTATTGGCCTTATGCAGGCATGCCTTGATGTTGTACTTCCATA
                                                   |  |   ||  | |||     ||| |  |     | | ||      ||||||||||||| |||||||| ||||| ||| |||| ||||||||||| ||  | || ||| | || || ||||| || ||| | || || || ||||| ||
--------------------------------------------gtgagtctgctgggtttcaagattgaacttgttaccagcagcgtatc----aacagGTGTTTATGTGATGATGTCTGGGCTGGATTTGGAGAGGCTTGTATTGGCATCTGGTCCTTTGGGTCTCATGCAAGCTTGCATGGACGTGGTTCTTCCCTA

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|148952108|gb|EC897900.2|EC897900
EST:     TGAGAACTGCTTTGTGCCATGCGAAAATGTCCTCGGTGAAGAAGGCAAAG                         GTGTTTATGTCATGATGTCAGGGCTTGATCTGGAAAGGCTTGTATTAGCTG
genomic: TGAGAACTGCTTTGTGCCATGCGAAAATGTCCTCGGTGAAGAAGGCAAAGgtattatctc ... cttgtggcagGTGTTTATGTCATGATGTCAGGGCTTGATCTGGAAAGGCTTGTATTAGCTG
EST: gi|24763821|gb|CA398992.1|CA398992
EST:     TGAGAACTGCTTTGTGCCATGCGAAAATGTCCTCGGTGAAGAAGGCAAAG                         GTGTTTATGTCATGATGTCAGGGCTTGATCTGGAAAGGCTTGTATTAGCTG
genomic: TGAGAACTGCTTTGTGCCATGCGAAAATGTCCTCGGTGAAGAAGGCAAAGgtattatctc ... cttgtggcagGTGTTTATGTCATGATGTCAGGGCTTGATCTGGAAAGGCTTGTATTAGCTG
EST: gi|148928298|gb|EE284912.2|EE284912
EST:     TGAGAACTGCTTTGTGCCATGCGAAAATGTCCTCGGTGAAGAAGGCAAAG                         GTGTTTATGTCATGATGTCAGGGCTTGATCTGGAAAGGCTTGTATTAGCTG
genomic: TGAGAACTGCTTTGTGCCATGCGAAAATGTCCTCGGTGAAGAAGGCAAAGgtattatctc ... cttgtggcagGTGTTTATGTCATGATGTCAGGGCTTGATCTGGAAAGGCTTGTATTAGCTG
EST: gi|37375704|gb|CF624307.1|CF624307
EST:     CCTCGGTGAAGAAGGCAAAG                         GTGTTTATGTCATGATGTCAGGGCTTGATCTGGAAAGGCTTGTATTAGCTG
genomic: CCTCGGTGAAGAAGGCAAAGgtattatctc ... cttgtggcagGTGTTTATGTCATGATGTCAGGGCTTGATCTGGAAAGGCTTGTATTAGCTG
EST: gi|148949902|gb|EC895400.2|EC895400
EST:     TGAGAACTGCTTTGTGCCATGCGAAAATGTCCTCGGTGAAGAAGGCAAAG                         GTGTTTATGTCATGATGTCAGGGCTTGATCTGGAAAGGCTTGTATTAGCTG
genomic: TGAGAACTGCTTTGTGCCATGCGAAAATGTCCTCGGTGAAGAAGGCAAAGgtattatctc ... cttgtggcagGTGTTTATGTCATGATGTCAGGGCTTGATCTGGAAAGGCTTGTATTAGCTG
EST: gi|31352282|gb|CD436639.1|CD436639
EST:     TGAGAACTGCTTTGTGCCATGCGAAAATGTCCTCGGTGAAGAAGGCAAAG                         GTGTTTATGTCATGATGTCAGGGCTTGATCTGGAAAGGCTTGTATTAGCTG
genomic: TGAGAACTGCTTTGTGCCATGCGAAAATGTCCTCGGTGAAGAAGGCAAAGgtattatctc ... cttgtggcagGTGTTTATGTCATGATGTCAGGGCTTGATCTGGAAAGGCTTGTATTAGCTG
EST: gi|60356707|gb|DN223680.1|DN223680
EST:     TGAGAACTGCTTTGTGCCATGCGAAAATGTCCTCGGTGAAGAAGGCAAAG                         GTGTTTATGTCATGATGTCAGGGCTTGATCTGGAAAGGCTTGTATTAGCTG
genomic: TGAGAACTGCTTTGTGCCATGCGAAAATGTCCTCGGTGAAGAAGGCAAAGgtattatctc ... cttgtggcagGTGTTTATGTCATGATGTCAGGGCTTGATCTGGAAAGGCTTGTATTAGCTG
EST: gi|8576983|gb|BE129620.1|BE129620
EST:     TCGGTGAAGAAGGCAAAG                         GTGTTTATGTCATGATGTCAGGGCTTGATCTGGAAAGGCTTGTATTAGCTG
genomic: TCGGTGAAGAAGGCAAAGgtattatctc ... cttgtggcagGTGTTTATGTCATGATGTCAGGGCTTGATCTGGAAAGGCTTGTATTAGCTG
EST: gi|40333885|gb|CK367955.1|CK367955
EST:     TGAGAACTGCTTTGTGCCATGCGAAAATGTCCTCGGTGAAGAAGGCAAAG                         GTGTTTATGTCATGATGTCAGGGCTTGATCTGGAAAGGCTTGTATTAGCTG
genomic: TGAGAACTGCTTTGTGCCATGCGAAAATGTCCTCGGTGAAGAAGGCAAAGgtattatctc ... cttgtggcagGTGTTTATGTCATGATGTCAGGGCTTGATCTGGAAAGGCTTGTATTAGCTG
EST: gi|16925518|gb|BM078586.1|BM078586
EST:     TGCGAAAATGT-CTCGGTGAAAGAAGGCAAAG                         GTGTTTATGTCATGATGTCAGGGCTTGATCTGGAAAGGCTTGTATTAGCTG
genomic: TGCGAAAATGTCCTCGGTG-AAGAAGGCAAAGgtattatctc ... cttgtggcagGTGTTTATGTCATGATGTCAGGGCTTGATCTGGAAAGGCTTGTATTAGCTG
EST: gi|37394249|gb|CF634396.1|CF634396
EST:     TGAGAACTGCTTTGTGCCATGCGAAAATGTCCTCGGTGAAGAAGGCAAAG                         GTGTTTATGTCATGATGTCAGGGCTTGATCTGGAAAGGCTTGTATTAGCTG
genomic: TGAGAACTGCTTTGTGCCATGCGAAAATGTCCTCGGTGAAGAAGGCAAAGgtattatctc ... cttgtggcagGTGTTTATGTCATGATGTCAGGGCTTGATCTGGAAAGGCTTGTATTAGCTG

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: 48 (upstream exon), 49 (downstream exon)
Score: 181

GTGTGAGCTTGTTTTTGAGAACTGCTTTGTGCCATGCGAAAATGTCCTCGGTGAAGAAGGCAAAGgtattatctc ... cttgtggcagGTGTTTATGTCATGATGTCAGGGCTTGATCTGGAAAGGCTTGTATTAGCTGCGGGCCCTATTGGCCTTATGCAGGCATGCCTTGATGTTGTACTTCCATA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 1415

GTGTGAGCTTGTTTTTGAGAACTGCTTTGTGCCATGCGAAAATGTCCTCGGTGAAGAAGGCAAAGgtattatctc ... cttgtggcagGTGTTTATGTCATGATGTCAGGGCTTGATCTGGAAAGGCTTGTATTAGCTGCGGGCCCTATTGGCCTTATGCAGGCATGCCTTGATGTTGTACTTCCATA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 699

GTGTGAGCTTGTTTTTGAGAACTGCTTTGTGCCATGCGAAAATGTCCTCGGTGAAGAAGGCAAAGgtattatctc ... cttgtggcagGTGTTTATGTCATGATGTCAGGGCTTGATCTGGAAAGGCTTGTATTAGCTGCGGGCCCTATTGGCCTTATGCAGGCATGCCTTGATGTTGTACTTCCATA


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 153

GTGTGAGCTTGTTTTTGAGAACTGCTTTGTGCCATGCGAAAATGTCCTCGGTGAAGAAGGCAAAGgtattatctc ... cttgtggcagGTGTTTATGTCATGATGTCAGGGCTTGATCTGGAAAGGCTTGTATTAGCTGCGGGCCCTATTGGCCTTATGCAGGCATGCCTTGATGTTGTACTTCCATA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aacagttctttaattggaggatcacctttgatctctatgccttttcttgtggcagGTGTTTATGTCATGATGTCAGGGCTTGATCTGGAAAGGCTTGTATTAGCTGCGGGCCCTATTGGCCTTATGCAGGCATGCCTTGATGTTGTACTTCCATA
                               tctctatgccttttct  CT-rich tract
     ttctttaatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gcagatgttcattccatgattttctaaaccccatataaagctagaaacagttctttaattggaggatcacctttgatctctatgccttttcttgtggcagGTGTTTATGTCATGATGTCAGGGCTTGATCTGGAAAGGCTTGTATTAGCTGCGGGCCCTATTGGCCTTATGCAGGCATGCCTTGATGTTGTACTTCCATA

gcagatg
- - - - - - - catgatt
- - - - - - - - - - - - - - - - - - - - - agaaacag