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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gcagatgtttattccacgattttctaaaccccatataaaactagaaagatttctttaattagatggtcacctttgatctctatgccttctcttgtggcagGTGTTTATGTCATGATGTCAGGGCTTGATCTGGAAAGGCTTGTATTAGCTGCGGGCCCTATTGGCCTTATGCAGGCATGCCTTGATGTTGTACTTCCATA

Basic information

species Zea mays
transcript GRMZM2G052630_T01
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G052630_T02 (Zea mays), 3'ss of exon 8
lower sequence: LOC_Os05g03480.4 (Oryza sativa), 3'ss of exon 9
-----------------------------------------------------------------------------gcagatgttt--attccacgattttcta--aaccccatataaaactagaaagattt----ctttaattagatggtcacctttgatctctatgc----cttctcttgtggcagGTGTTTATGTCATGATGTCAGGGCTTGATCTGGAAAGGCTTGTATTAGCTGCGGGCCCTATTGGCCTTATGCAGGCATGCCTTGATGTTGTACTTCCATA
                                                                              ||| |||||  ||    | |  | | |     | || | ||||||   |  |||     | || ||    |  ||| | |  |    |   |     || |||||| ||||||||||||||||||||||||||||||||||| ||||| ||||| |||||||| || ||||| ||||| ||||| |||||||||||||| |   |||| ||
gtattaactgctgattgtcgtaaacttagtcagaattcttgttgctatcctgagatatttattcagttgtgtacagtacagttgtttgcatctaccaaactgccactgtacacacagaaaactgtcataattctagccattgatcctgttatcatcctcaaagagtgaacagtttttttcttgttgcagGTGTTTATGTCATGATGTCAGGGCTTGATCTAGAAAGACTTGTGTTAGCTGCAGGTCCTATCGGCCTCATGCAAGCATGCCTTGATGTAGCTGTTCCTTA

upper sequence: GRMZM2G052630_T02 (Zea mays), 3'ss of exon 8
lower sequence: GLYMA12G07570.1 (Glycine max), 3'ss of exon 10
gcagatgtttattccacgattttcta---aaccccatataaaactagaaagatttcttta--attagatggtca---cctttgatctctatgccttctcttgtggcagGTGTTTATGTCATGATGTCAGGGCTTGATCTGGAAAGGCTTGTATTAGCTGCGGGCCCTATTGGCCTTATGCAGGCATGCCTTGATGTTGTACTTCCATA
        |  || | |  ||||| |   ||   |  |||||   |   | ||||  |||   ||  |||   |    | || ||  | |    |||| ||||  |||| || |||||||||||||| ||||| |||||||| || ||||| || || || || ||| ||||  ||||||||||||| ||||||||||| ||||| ||
--------tcctttctcttttttccatgcaaatactgataaagagaaggacattttgttattgttgcatgtcaagtgtcatttattaccacttattcttttgtttcagGAGTCTATGTCATGATGTCTGGGCTGGATCTGGAGAGACTTGTTTTGGCAGCTGGTCCTCTTGGTATTATGCAGGCATGTCTTGATGTTGTCCTTCCTTA

upper sequence: GRMZM2G052630_T02 (Zea mays), 3'ss of exon 8
lower sequence: GLYMA11G15900.1 (Glycine max), 3'ss of exon 10
gcagatgtttattccacgattttctaaaccccatataaaactagaaagatttcttta--attagatggtcacctttgatctctatgccttctcttgtgg---cagGTGTTTATGTCATGATGTCAGGGCTTGATCTGGAAAGGCTTGTATTAGCTGCGGGCCCTATTGGCCTTATGCAGGCATGCCTTGATGTTGTACTTCCATA
     |  |  ||   | ||   | || ||  ||  |||   |  || ||||  |||   ||  |||   |   |   ||  |||  ||| |  | |||   |||| || |||||||||||||| ||||| |||||||| || ||||| || || || || ||| ||||  ||||||||||||| |||||||| || ||||| ||
---ctttctcttttttcaatg--caaatcctgattaaaagggaagaacatttagttattgttgcatgtcaagtgtcattcattatcacttattctttggtttcagGAGTCTATGTCATGATGTCTGGGCTGGATCTGGAGAGACTTGTTTTGGCAGCTGGTCCTCTTGGTATTATGCAGGCATGTCTTGATGTCGTCCTTCCTTA

upper sequence: GRMZM2G052630_T02 (Zea mays), 3'ss of exon 8
lower sequence: Vv06s0004g03140.t01 (Vitis vinifera), 3'ss of exon 10
gcagatgtttattccacgattttctaaaccccatataaaactagaaagatttctttaattagatggtcacct----ttgatctctatgccttctcttgtggcagGTGTTTATGTCATGATGTCAGGGCTTGATCTGGAAAGGCTTGTATTAGCTGCGGGCCCTATTGGCCTTATGCAGGCATGCCTTGATGTTGTACTTCCATA
       |||||  || | || | | |     || ||  | || |   | ||||||  ||   |  ||  ||    ||||  |   || | | | |  |  |||| ||||| || |||||||||||||| ||| ||||||||||||| || || || || ||  |||| ||||||||||||||  | ||||| || ||||| ||
-tgagcatttatcaca-gcttatatgattgtaatttatta-taaatgaacttcttttcttttttcttcttctaatattgacattgttgtcctttttcttt-cagGAGTTTACGTAATGATGTCAGGGCTAGATTTGGAAAGGCTTGTTTTGGCAGCTGGGCCCCTTGGTCTTATGCAGGCATGTATAGATGTAGTTCTTCCCTA

upper sequence: GRMZM2G052630_T02 (Zea mays), 3'ss of exon 8
lower sequence: EFJ09244 (Selaginella moellendorffii), 3'ss of exon 11
gcagatgtttattccacgattttctaaaccccatataaaactagaaagatttctttaattagatggtcacctttgatctctatgccttctcttgtggcagGTGTTTATGTCATGATGTCAGGGCTTGATCTGGAAAGGCTTGTATTAGCTGCGGGCCCTATTGGCCTTATGCAGGCATGCCTTGATGTTGTACTTCCATA
                                                 |||  |   ||  | | |     ||| |        | | ||      ||||||||||||| |||||||| ||||| ||| |||| ||||||||||| ||  | || ||| | || || ||||| || ||| | || || || ||||| ||
--------------------------------------------gtgagtttgctgggtttcaagattgaacttgttactagcagcgtatc----aacagGTGTTTATGTGATGATGTCTGGGCTGGATTTGGAGAGGCTTGTATTGGCATCTGGTCCTTTGGGTCTCATGCAAGCTTGCATGGACGTGGTTCTTCCCTA

upper sequence: GRMZM2G052630_T02 (Zea mays), 3'ss of exon 8
lower sequence: EFJ07135 (Selaginella moellendorffii), 3'ss of exon 11
gcagatgtttattccacgattttctaaaccccatataaaactagaaagatttctttaattagatggtcacctttgatctctatgccttctcttgtggcagGTGTTTATGTCATGATGTCAGGGCTTGATCTGGAAAGGCTTGTATTAGCTGCGGGCCCTATTGGCCTTATGCAGGCATGCCTTGATGTTGTACTTCCATA
                                                 | |  |   ||  | | |     ||| |  |     | | ||      ||||||||||||| |||||||| ||||| ||| |||| ||||||||||| ||  | || ||| | || || ||||| || ||| | || || || ||||| ||
--------------------------------------------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|67030645|gb|CO459394.1|CO459394
EST:     TGAGAACTGCTTTGTGCCACGCGAGAATGTCCTCGGTGAAGAAGGCAA-G                         GTGTTTATGTCATGATGTCAGGGCTTGATCTGGAAAAGCTTGTATTA
genomic: TGAGAACTGCTTTGTGCCACGCGAGAATGTCCTCGGTGAAGAAGGCAAAGgtattgcctc ... cttgtggcagGTGTTTATGTCATGATGTCAGGGCTTGATCTGGAAAGGCTTGTATTA
EST: gi|24769404|gb|CA404533.1|CA404533
EST:     ACGCGAGAATGTCCTCGGTGAAGAAGGCAAAG                         GTGTTTATGTCATGATGTCAGGGCTTGATCTGGAAAGGCTTGTATTAGCTG
genomic: ACGCGAGAATGTCCTCGGTGAAGAAGGCAAAGgtattgcctc ... cttgtggcagGTGTTTATGTCATGATGTCAGGGCTTGATCTGGAAAGGCTTGTATTAGCTG
EST: gi|110190881|gb|EC872779.1|EC872779
EST:     GTGAAGAAGGCAAAG                         GTGTTTATGTCATGATGTCAGGGCTTGATCTGGAAAGGCTTGTATTAGCTG
genomic: GTGAAGAAGGCAAAGgtattgcctc ... cttgtggcagGTGTTTATGTCATGATGTCAGGGCTTGATCTGGAAAGGCTTGTATTAGCTG
EST: gi|31354622|gb|CD438979.1|CD438979
EST:     TGAGAACTGCTTTGTGCCACGCGAGAATGTCCTCGGTGAAGAAGGCAAAG                         GTGTTTATGTCATGATGTCAGGGCTTGATCTGGAAAGGCTTGTATTAGCTG
genomic: TGAGAACTGCTTTGTGCCACGCGAGAATGTCCTCGGTGAAGAAGGCAAAGgtattgcctc ... cttgtggcagGTGTTTATGTCATGATGTCAGGGCTTGATCTGGAAAGGCTTGTATTAGCTG
EST: gi|76936508|gb|DV174756.1|DV174756
EST:     TGAGAACTGCTTTGTGCCACGCGAGAATGTCCTCGGTGAAGAAGGCAAAG                         GTGTTTATGTCATGATGTCAGGGCTTGATCTGGAAAGGCTTGTATTAGCTG
genomic: TGAGAACTGCTTTGTGCCACGCGAGAATGTCCTCGGTGAAGAAGGCAAAGgtattgcctc ... cttgtggcagGTGTTTATGTCATGATGTCAGGGCTTGATCTGGAAAGGCTTGTATTAGCTG
EST: gi|78105056|gb|DV523474.1|DV523474
EST:     TGAGAACTGCTTTGTGCCACGCGAGAATGTCCTCGGTGAAGAAGGCAAAG                         GTGTTTATGTCATGATGTCAGGGCTTGATCTGGAAAGGCTTGTATTAGCTG
genomic: TGAGAACTGCTTTGTGCCACGCGAGAATGTCCTCGGTGAAGAAGGCAAAGgtattgcctc ... cttgtggcagGTGTTTATGTCATGATGTCAGGGCTTGATCTGGAAAGGCTTGTATTAGCTG
EST: gi|149079538|gb|EE168523.2|EE168523
EST:     TGAGAACTGCTTTGTGCCACGCGAGAATGTCCTCGGTGAAGAAGGCAAAG                         GTGTTTATGTCATGATG
genomic: TGAGAACTGCTTTGTGCCACGCGAGAATGTCCTCGGTGAAGAAGGCAAAGgtattgcctc ... cttgtggcagGTGTTTATGTCATGATG
EST: gi|31360769|gb|CD445126.1|CD445126
EST:     TGAGAACTGCTTTGTGCCACGCGAGAATGTCCTCGGTGAAGAAGGCAAAG                         GTGTTTATGTCATGATGTCAGGGCTTGATCTGGAAAGGCTTGTATTAGCTG
genomic: TGAGAACTGCTTTGTGCCACGCGAGAATGTCCTCGGTGAAGAAGGCAAAGgtattgcctc ... cttgtggcagGTGTTTATGTCATGATGTCAGGGCTTGATCTGGAAAGGCTTGTATTAGCTG
EST: gi|60347547|gb|DN214520.1|DN214520
EST:     TGAGAACTGCTTTGTGCCACGCGAGAATGTCCTCGGTGAAGAAGGCAAAG                         GTGTTTATGTCATGATGTCAGGGCTTGATCTGGAAAGGCTTGTATTAGCTG
genomic: TGAGAACTGCTTTGTGCCACGCGAGAATGTCCTCGGTGAAGAAGGCAAAGgtattgcctc ... cttgtggcagGTGTTTATGTCATGATGTCAGGGCTTGATCTGGAAAGGCTTGTATTAGCTG
EST: gi|74240406|gb|DT648320.1|DT648320
EST:     TGAGAACTGCTTTGTGCCACGCGAGAATGTCCTCGGTGAAGAAGGCAAAG                         GTGTTTATGTCATGATGTCAGGGCTTGATCTGGAAAGGCTTGTATTAGCTG
genomic: TGAGAACTGCTTTGTGCCACGCGAGAATGTCCTCGGTGAAGAAGGCAAAGgtattgcctc ... cttgtggcagGTGTTTATGTCATGATGTCAGGGCTTGATCTGGAAAGGCTTGTATTAGCTG
EST: gi|76936507|gb|DV174755.1|DV174755
EST:     TGAGAACTGCTTTGTGCCACGCGAGAATGTCCTCGGTGAAGAAGGCAAAG                         GTGTTTATGTCATGATGTCAGGGCTTGATCTGGAAAGGCTTGTATTAGCTG
genomic: TGAGAACTGCTTTGTGCCACGCGAGAATGTCCTCGGTGAAGAAGGCAAAGgtattgcctc ... cttgtggcagGTGTTTATGTCATGATGTCAGGGCTTGATCTGGAAAGGCTTGTATTAGCTG
EST: gi|91057188|gb|EB167606.1|EB167606
EST:     TGAGAACTGCTTTGTGCCACGCGAGAATGTCCTCGGTGAAGAAGGCAAAG                         GTGTTTATGTCATGATGTCAGGGCTTGATCTGGAAAGGCTTGTATTAGCTG
genomic: TGAGAACTGCTTTGTGCCACGCGAGAATGTCCTCGGTGAAGAAGGCAAAGgtattgcctc ... cttgtggcagGTGTTTATGTCATGATGTCAGGGCTTGATCTGGAAAGGCTTGTATTAGCTG
EST: gi|149073457|gb|EE161762.2|EE161762
EST:     TGAGAACTGCTTTGTGCCACGCGAGAATGTCCTCGGTGAAGAAGGCAAAG                         GTGTTTATGTCATGATGTCCAGGCCTTGATCTGGAAAGGCCTTGTATTTA-
genomic: TGAGAACTGCTTTGTGCCACGCGAGAATGTCCTCGGTGAAGAAGGCAAAGgtattgcctc ... cttgtggcagGTGTTTATGTCATGATGTC-AGGGCTTGATCTGGAAAGGC-TTGTATT-AG
EST: gi|110525230|gb|EE029414.1|EE029414
EST:     TGAGAACTGCTTTGTGCCACGCGAGAATGTCCTCGGTGAAGAAGGCAAAG                         GTGTTTATGTCATGATGTCAGGGCTTGATCTGGAAAGGCTTGTATTAGCTG
genomic: TGAGAACTGCTTTGTGCCACGCGAGAATGTCCTCGGTGAAGAAGGCAAAGgtattgcctc ... 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: 47 (upstream exon), 49 (downstream exon)
Score: 142

ATGTGAGCTTGTTTTTGAGAACTGCTTTGTGCCACGCGAGAATGTCCTCGGTGAAGAAGGCAAAGgtattgcctc ... cttgtggcagGTGTTTATGTCATGATGTCAGGGCTTGATCTGGAAAGGCTTGTATTAGCTGCGGGCCCTATTGGCCTTATGCAGGCATGCCTTGATGTTGTACTTCCATA


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 749

ATGTGAGCTTGTTTTTGAGAACTGCTTTGTGCCACGCGAGAATGTCCTCGGTGAAGAAGGCAAAGgtattgcctc ... cttgtggcagGTGTTTATGTCATGATGTCAGGGCTTGATCTGGAAAGGCTTGTATTAGCTGCGGGCCCTATTGGCCTTATGCAGGCATGCCTTGATGTTGTACTTCCATA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 426

ATGTGAGCTTGTTTTTGAGAACTGCTTTGTGCCACGCGAGAATGTCCTCGGTGAAGAAGGCAAAGgtattgcctc ... cttgtggcagGTGTTTATGTCATGATGTCAGGGCTTGATCTGGAAAGGCTTGTATTAGCTGCGGGCCCTATTGGCCTTATGCAGGCATGCCTTGATGTTGTACTTCCATA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 167

ATGTGAGCTTGTTTTTGAGAACTGCTTTGTGCCACGCGAGAATGTCCTCGGTGAAGAAGGCAAAGgtattgcctc ... cttgtggcagGTGTTTATGTCATGATGTCAGGGCTTGATCTGGAAAGGCTTGTATTAGCTGCGGGCCCTATTGGCCTTATGCAGGCATGCCTTGATGTTGTACTTCCATA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aagatttctttaattagatggtcacctttgatctctatgccttctcttgtggcagGTGTTTATGTCATGATGTCAGGGCTTGATCTGGAAAGGCTTGTATTAGCTGCGGGCCCTATTGGCCTTATGCAGGCATGCCTTGATGTTGTACTTCCATA
                               tctctatgccttctct  CT-rich tract
     ttctttaattagat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gcagatgtttattccacgattttctaaaccccatataaaactagaaagatttctttaattagatggtcacctttgatctctatgccttctcttgtggcagGTGTTTATGTCATGATGTCAGGGCTTGATCTGGAAAGGCTTGTATTAGCTGCGGGCCCTATTGGCCTTATGCAGGCATGCCTTGATGTTGTACTTCCATA

gcagatg