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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tttaatgtatcctttgtttatgtgcatatggctgtacccagtcctcccctggtgtgcgcgtgttttttccttgtgaacattctgtagttattctcttcagGAGCCGTGAATTTCTGTGGCAAGAGGGGCATACTGCTTTTGCGACTAAAGAAGAGGCAGATGAAGAG

Basic information

species Zea mays
transcript GRMZM2G094123_T01
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G094123_T01 (Zea mays), 3'ss of exon 5
lower sequence: LOC_Os12g25710.3 (Oryza sativa), 3'ss of exon 5
tttaatgtatcctttgtttatgtgcatatggctg---tacccagtcctcccctggtgtgcgcgtgttttttccttgtga-acattctgtagttattctcttcagGAGCCGTGAATTTCTGTGGCAAGAGGGGCATACTGCTTTTGCGACTAAAGAAGAGGCAGATGAAGAG
     ||| ||| | | |   |   |  ||| ||   ||  || |        ||  |       |  | ||    ||| ||||||||||  |||||||  |||||||||||| || || |||||||| |||||||| |||||||| |||||||| ||||| || ||||||
---cctgtttccat-gatggcgaataggtggttgacctatgcactagggaatagggatatattcatcatctctggctgacacattctgtaactattctccgcagGAGCCGTGAGTTCCTTTGGCAAGAAGGGCATACAGCTTTTGCAACTAAAGAGGAGGCTGACGAAGAG

upper sequence: GRMZM2G094123_T01 (Zea mays), 3'ss of exon 5
lower sequence: GLYMA03G38340.1 (Glycine max), 3'ss of exon 6
tttaatgtatcctttgtttatgt-gcatatggctgtacccagtcctcccctggtgtgcgcgtgttttttccttgtgaacattctgtagttattctctt-cagGAGCCGTGAATTTCTGTGGCAAGAGGGGCATACTGCTTTTGCGACTAAAGAAGAGGCAGATGAAGAG
 ||||| |    || | |  ||| || |     |  |     |  |   ||||       ||  |  | | |||||       | |||   ||   || |||||| ||||| ||||| |||||||| ||||| |||||||||||  | || || || ||||||| ||||
-ttaatatggttttggatactgttgctttcatgtaaaatagtttatattctggaac-tttgtcctagtccattgtgtggtgcttatagaagtttgattgcagGAGTCGTGAGTTTCTTTGGCAAGAAGGGCACACTGCTTTTGCTTCAAAGGAGGAAGCAGATGCAGAG

upper sequence: GRMZM2G094123_T01 (Zea mays), 3'ss of exon 5
lower sequence: AT5G10880.1 (Arabidopsis thaliana), 3'ss of exon 2
tttaatgtatcctttgtttatgtgcatatggctgtacccagtcctcccctggtgtgcgcgtgttttttccttgtgaacattctgtagttattctcttcagGAGCCGTGAATTTCTGTGGCAAGAGGGGCATACTGCTTTTGCGACTAAAGAAGAGGCAGATGAAGAG-----------------------------------------------------------------------------------------------------------------------------
                       |   |    ||   | | |  | |  || |    | | ||||       | || | | |   | ||||      |||||||||||| || || |||||||| || || |||| |||||| || ||||||||||| ||||| |||                                                                                                                             
-----------------------gttaaccagtg-ggctaatgttacgttgttagatgggagttta------gcgaccctaccccatttat------caggagccgtgagttcctttggcaagaaggacacactgattttgctaccaaagaagaggctgatgaggaggtgcttgatgtttgaacatctacagCCGCGTGTATGACTCATGGAGATGACAAAGGTTTAGTATTCCCTCCTAAAGTGGCACCTGTTCAAGTTGTTGTAATCCATGTTCCCATCAAAGGCGCTGC

upper sequence: GRMZM2G094123_T01 (Zea mays), 3'ss of exon 5
lower sequence: Vv07s0005g02620.t01 (Vitis vinifera), 3'ss of exon 6
-------tttaatgt-atcctttgtttatgtgcatatggctgtacccagtcctcccctggtgtgcgcgtgttttttccttgtgaacattctgtagttattctcttcagGAGCCGTGAATTTCTGTGGCAAGAGGGGCATACTGCTTTTGCGACTAAAGAAGAGGCAGATGAAGAG
       |  | | | || ||    ||   |   | |   | |    |    ||     || |    ||   ||  ||| || ||||| || |  |  || |    ||||| || |||||||| ||||| |||||||||||||||||||| || || |||||||||||| |||||
ttcatgatcgactatgattctccaattccttatttgttaatatgttaaaaaatctt---gtttagttgttcattggcctagttaacatact-tgatggttgt----agGAGTCGGGAATTTCTTTGGCAGGAGGGGCATACTGCTTTTGCTACAAAGGAAGAGGCAGATAAAGAG

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|71332073|gb|DR802941.1|DR802941
EST:     TGGTGTAATGTTGTTAGATGGGAGTTTAGCAATCCAACTCCTTTCATAAG                         GAGCCGTGAATTTCTGTGGCAAGAGGGGCATACTGCTTTTGCGACTAAAGA
genomic: TGGTGTAATGTTGTTAGATGGGAGTTTAGCAATCCAACTCCTTTCATAAGgtacctcatt ... ttctcttcagGAGCCGTGAATTTCTGTGGCAAGAGGGGCATACTGCTTTTGCGACTAAAGA
EST: gi|7031274|gb|AW461012.1|AW461012
EST:     TGTTACATGGGAGTTTAGCAATCCAACTCCTTTCATAAG                         GAGCCGTGAATTTCTGTGGCAAGAGGGGCATACTGCTTTTGCGACTAAAGA
genomic: TGTTAGATGGGAGTTTAGCAATCCAACTCCTTTCATAAGgtacctcatt ... ttctcttcagGAGCCGTGAATTTCTGTGGCAAGAGGGGCATACTGCTTTTGCGACTAAAGA
EST: gi|6865183|gb|AW360533.1|AW360533
EST:     TGGTGTAATGTTGTTAGATGGGAGTTTAGCAATCCAACTCCTTTCATAAG                         GAGCCGTGAATTTCTGTGGCAAGAGGGGCATACTGCTTTTGCGACTAAAGA
genomic: TGGTGTAATGTTGTTAGATGGGAGTTTAGCAATCCAACTCCTTTCATAAGgtacctcatt ... ttctcttcagGAGCCGTGAATTTCTGTGGCAAGAGGGGCATACTGCTTTTGCGACTAAAGA
EST: gi|211280528|gb|FL042846.1|FL042846
EST:     GTGTAATGTTGTTAGGATGGGGAGTTTAGCAATCCAACTCCTTTCATAAG                         GAGCCGTGATTTTCTGTGGGCA-GAGGGGCATACTGCTTTTTGCGACTAAA
genomic: GTGTAATGTTGTTAG-ATGGG-AGTTTAGCAATCCAACTCCTTTCATAAGgtacctcatt ... ttctcttcagGAGCCGTGAATTTCTGTGG-CAAGAGGGGCATACTGCTTTT-GCGACTAAA
EST: gi|67027739|gb|CO456488.1|CO456488
EST:     TGGTGTAATGTTGTTAGATGGGAGTTTAGCAATCCAACTCCTTTCATAAG                         GAGCCGTGAATTTCTGTGGCAAGAGGGGCATACTGCTTTTGCGACTAAAGA
genomic: TGGTGTAATGTTGTTAGATGGGAGTTTAGCAATCCAACTCCTTTCATAAGgtacctcatt ... ttctcttcagGAGCCGTGAATTTCTGTGGCAAGAGGGGCATACTGCTTTTGCGACTAAAGA
EST: gi|31359187|gb|CD443544.1|CD443544
EST:     TGGTGTAATGTTGTTAGATGGGAG-TTAGCAATCCAACTCCTTTCATAAG                         GAGCCGTGAATTTCTGTGGCAAGAGGGGCATACTGCTTTTGCGACTAAAGA
genomic: TGGTGTAATGTTGTTAGATGGGAGTTTAGCAATCCAACTCCTTTCATAAGgtacctcatt ... ttctcttcagGAGCCGTGAATTTCTGTGGCAAGAGGGGCATACTGCTTTTGCGACTAAAGA
EST: gi|67020078|gb|CO448827.1|CO448827
EST:     GATGGGA-TTTAGCAATCCAAGTCCTCTTC-TAAG                         GAGCCGAAAATTTCTGTGGCAAGAGGGGCATACTGCTTTTGCGACTAAAG
genomic: GATGGGAGTTTAGCAATCCAACTCCT-TTCATAAGgtacctcatt ... ttctcttcagGAGCCGTGAATTTCTGTGGCAAGAGGGGCATACTGCTTTTGCGACTAAAG
EST: gi|67027210|gb|CO455959.1|CO455959
EST:     TGGTGTAATGTTGTTAGATGGGAGTTTAGCAATCCAACTCCTTTCATAAG                         GAGCCGTGAATTTCTGTGGCAAGAGGGGCATACTGCTTTTGCGACTAAAGA
genomic: TGGTGTAATGTTGTTAGATGGGAGTTTAGCAATCCAACTCCTTTCATAAGgtacctcatt ... ttctcttcagGAGCCGTGAATTTCTGTGGCAAGAGGGGCATACTGCTTTTGCGACTAAAGA
EST: gi|32929788|gb|CF034600.1|CF034600
EST:     TGGTGTAATGTTGTTAGATGGGAGTTTAGCAATCCAACTCCTTTCATAAG                         GAGCCGTGAATTTCTGTGGCAAGAGGGGCATACTGCTTTTGCGACTAAAGA
genomic: TGGTGTAATGTTGTTAGATGGGAGTTTAGCAATCCAACTCCTTTCATAAGgtacctcatt ... ttctcttcagGAGCCGTGAATTTCTGTGGCAAGAGGGGCATACTGCTTTTGCGACTAAAGA

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), 48 (downstream exon)
Score: 295

TCTCCAAATGGATAAGAAGCCACCGAGACTTACCCTTGAGGTGTAATCAATGGTGTAATGTTGTTAGATGGGAGTTTAGCAATCCAACTCCTTTCATAAGgtacctcatt ... ttctcttcagGAGCCGTGAATTTCTGTGGCAAGAGGGGCATACTGCTTTTGCGACTAAAGAAGAGGCAGATGAAGAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 252

TCTCCAAATGGATAAGAAGCCACCGAGACTTACCCTTGAGGTGTAATCAATGGTGTAATGTTGTTAGATGGGAGTTTAGCAATCCAACTCCTTTCATAAGgtacctcatt ... ttctcttcagGAGCCGTGAATTTCTGTGGCAAGAGGGGCATACTGCTTTTGCGACTAAAGAAGAGGCAGATGAAGAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 238

TCTCCAAATGGATAAGAAGCCACCGAGACTTACCCTTGAGGTGTAATCAATGGTGTAATGTTGTTAGATGGGAGTTTAGCAATCCAACTCCTTTCATAAGgtacctcatt ... ttctcttcagGAGCCGTGAATTTCTGTGGCAAGAGGGGCATACTGCTTTTGCGACTAAAGAAGAGGCAGATGAAGAG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 209

TCTCCAAATGGATAAGAAGCCACCGAGACTTACCCTTGAGGTGTAATCAATGGTGTAATGTTGTTAGATGGGAGTTTAGCAATCCAACTCCTTTCATAAGgtacctcatt ... ttctcttcagGAGCCGTGAATTTCTGTGGCAAGAGGGGCATACTGCTTTTGCGACTAAAGAAGAGGCAGATGAAGAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cccctggtgtgcgcgtgttttttccttgtgaacattctgtagttattctcttcagGAGCCGTGAATTTCTGTGGCAAGAGGGGCATACTGCTTTTGCGACTAAAGAAGAGGCAGATGAAGAG
                                          ttattctcttc  CT-rich tract
               tgtttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tttaatgtatcctttgtttatgtgcatatggctgtacccagtcctcccctggtgtgcgcgtgttttttccttgtgaacattctgtagttattctcttcagGAGCCGTGAATTTCTGTGGCAAGAGGGGCATACTGCTTTTGCGACTAAAGAAGAGGCAGATGAAGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - -tgtatcc
- - - - - - - - - - -gtgcata
- - - - - - - - - - - - - - - gctgtac
- - - - - - - - - - - - - - - - - - - - - - - -cctggtg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -cattctg