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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagttctatgataccttattgtgatttatggtatttcctatatgatttgacaccccttgttcttttttgtagATTCTGGGCAGTGGAATGTCAAATAAGATGTGGGACAGCCTTGTTGATCATGCAAAGACGTGTGTCTTAAGTGGAAAGCATTATGTATACTATGCTAGAG

Basic information

species Zea mays
transcript GRMZM2G054109_T01
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G054109_T01 (Zea mays), 3'ss of exon 6
lower sequence: LOC_Os02g35470.3 (Oryza sativa), 3'ss of exon 6
gtaagttctatgat-------accttattgtgatttatggtatttcctatatgatttgacaccccttgttcttttttgtagATTCTGGGCAGTGGAATGTCAAATAAGATGTGGGACAGCCTTGTTGATCATGCAAAGACGTGTGTCTTAAGTGGAAAGCATTATGTATACTATGCTAGAG
||||||||||  ||       |     |||| ||| |||   |||  |  |||||   | ||| ||| ||  ||||   ||||||| ||||||||||||||||||||||||||||| ||||||||||| ||||||||||| |||||||||||||||||||| |||||||| |||||||  |
gtaagttctacaattgttgttaataggttgtaattaatgtagtttaattgatgatcaaatacctcttttttctttt---agATTCTTGGCAGTGGAATGTCAAATAAGATGTGGGAAAGCCTTGTTGAGCATGCAAAGACTTGTGTCTTAAGTGGAAAGCACTATGTATATTATGCTATTG

upper sequence: GRMZM2G054109_T01 (Zea mays), 3'ss of exon 6
lower sequence: GLYMA15G07330.1 (Glycine max), 3'ss of exon 5
--------------------------------gtaagttcta----tgataccttattgtgatttatggtatttc-ctatatga---tttgacaccccttgttcttttttgtagATTCTGGGCAGTGGAATGTCAAATAAGATGTGGGACAGCCTTGTTGATCATGCAAAGACGTGTGTCTTAAGTGGAAAGCATTATGTATACTATGCTAGAG
                                   ||||  |    ||||      | ||||| ||   | |||  ||||   |   ||| ||        |    |  |||||||||| || ||||| |||||||| || ||||||||    || ||||| ||||||||||| |||||  | |||||||| |  |||||||||||| |    |
gtaagaatctatagacactttttctcatgggaaagagtttcaagtttgatttgacttggtgatataaattttttaactatccaaaattttcacggattaactatcctcatgtagATTCTTGGGAGTGGCATGTCAAACAAAATGTGGGATGTTCTAGTTGAGCATGCAAAGACTTGTGTTCTTAGTGGAAAACTCTATGTATACTATCCCGATG

upper sequence: GRMZM2G054109_T01 (Zea mays), 3'ss of exon 6
lower sequence: GLYMA07G30990.2 (Glycine max), 3'ss of exon 4
-----------------------------------------gtaagttctatgat-accttattgtgatttatggtatttcctatatgatttgacacccct-----tgttcttttttgtagATTCTGGGCAGTGGAATGTCAAATAAGATGTGGGACAGCCTTGTTGATCATGCAAAGACGTGTGTCTTAAGTGGAAAGCATTATGTATACTATGCTAGAG
                                          |   |   ||| | |  |  || || ||| |  |     | ||   || | |      |     |  |  || ||||||||||| || ||||| |||||||||||||||||||| |  |||||||| || |||||||| |||||  | |||||||| | ||| ||||||||| ||  ||
gtaagaatccagatttttgtccatttaggattttaatgtcaattgatctaatgctcaattccttttggtttgtatttgaatcgatgatatataattattttatggatacttcttattgtagATTCTTGGGAGTGGCATGTCAAATAAGATGTGGGATATTCTTGTTGAGCACGCAAAGACTTGTGTTCTCAGTGGAAAACTTTACGTATACTATCCTGAAG

upper sequence: GRMZM2G054109_T01 (Zea mays), 3'ss of exon 6
lower sequence: GLYMA08G06320.1 (Glycine max), 3'ss of exon 5
----------------------------------------------------------------gtaagttctatgataccttattgtg---atttatggtatttcctatatgattt-----gacaccccttgttcttttttgtagATTCTGGGCAGTGGAATGTCAAATAAGATGTGGGACAGCCTTGTTGATCATGCAAAGACGTGTGTCTTAAGTGGAAAGCATTATGTATACTATGCTAGAG
                                                                 | | || |||   |  | ||  ||   | ||||  ||| |   | | |||||     |  | |  |  ||| || ||||||||||| || || || |||||||||||||||||||| |  |||||||| ||||||||||| |||||  | |||||||| | ||||||||||||| ||   |
gtaagaatctagatttttgtccatttaggattttaatgtcaattgaccaaatgttcaattctttttgatttgtatttgaattgatgatgtaaaattattttatatgtcaaaggatttatttggttaactatacttccttattgtagATTCTTGGGAGCGGCATGTCAAATAAGATGTGGGATATTCTTGTTGAGCATGCAAAGACTTGTGTTCTCAGTGGAAAACTTTATGTATACTATCCTGATG

upper sequence: GRMZM2G054109_T01 (Zea mays), 3'ss of exon 6
lower sequence: AT4G25800.1 (Arabidopsis thaliana), 3'ss of exon 6
-------------------gtaagttctatgataccttattgtga--tttatggtatttcctatatgatttgacaccccttgttcttttttgtagATTCTGGGCAGTGGAATGTCAAATAAGATGTGGGACAGCCTTGTTGATCATGCAAAGACGTGTGTCTTAAGTGGAAAGCATTATGTATACTATGCTAGAG
                     ||| ||  || |     ||    |  || ||   ||   |   |  | ||   |    ||| | ||| |  |||||||| || ||||| ||||||||||||||||||||    || || || |||||||| || |||||| |||| || |||| |||| | |||||| ||  ||
gtgagtgcctcctattacgtcaagctcattgttgttggatgagaacattcattcaatgctcatgagtaattatgattatttgatatttgtc-tagATTCTTGGAAGTGGCATGTCAAATAAGATGTGGGATTTGCTAGTGGAGCATGCAAAAACATGTGTCCTAAGCGGTAAGCTTTATATCTACTATACTGAAG

upper sequence: GRMZM2G054109_T01 (Zea mays), 3'ss of exon 6
lower sequence: Vv11s0052g01380.t01 (Vitis vinifera), 3'ss of exon 5
gtaagttctatgataccttattgt----gatttatggtatttcctatatgatt--tgacaccccttgttcttttttgtagATTCTGGGCAGTGGAATGTCAAATAAGATGTGGGACAGCCTTGTTGATCATGCAAAGACGTGTGTCTTAAGTGGAAAGCATTATGTATACTATGCTAGAG
|||||| | ||  |   ||  ||     ||  ||   |  |       || ||  ||| |    ||  |  ||  ||||||| ||||| ||||| ||||||||||||||||||||    ||| | || ||||||||||| ||   | | |||||||||   ||||| || ||| ||   |
gtaagtgcaatatttagttgctgaattagaaatacaatgatctaatcttgtttcctgatatatttttctggttgctgtagATCCTGGGAAGTGGCATGTCAAATAAGATGTGGGAGGCTCTTATAGAGCATGCAAAGACTTGCACCATGAGTGGAAAGTTCTATGTTTATTATTCTGATG

upper sequence: GRMZM2G054109_T01 (Zea mays), 3'ss of exon 6
lower sequence: Vv00s0181g00220.t01 (Vitis vinifera), 3'ss of exon 7
------gtaagttctatgataccttattgtgatttatggtatttcctatatgatttgacaccccttgttct---tttttgtagATTCTGGGCAGTGGAATGTCAAATAAGATGTGGGACAGCCTTGTTGATCATGCAAAGACGTGTGTCTTAAGTGGAAAGCATTATGTATACTATGCTAGAG
       |      | || |  | | |    ||||    |   ||   | | ||||        ||||      || ||||||||||| || ||||| ||||||||||||||||||||    ||||| || |||||||| || |||||  ||||||| || | |||||| |||||| ||   |
gtaagaatgtacattttgttgtcatttcagaatttg-aatccgtctattgtaatttttatttatttgtctccaattgttgtagATTCTTGGAAGTGGCATGTCAAATAAGATGTGGGATGTTCTTGTGGAGCATGCAAAAACTTGTGTTCTAAGTGGGAAACTTTATGTTTACTATCCTGATG

upper sequence: GRMZM2G054109_T01 (Zea mays), 3'ss of exon 6
lower sequence: EFJ34469 (Selaginella moellendorffii), 3'ss of exon 5
gtaagttctatgataccttattgtgatttatggtatttcctatatgatttgacaccccttgttcttttttgtagATTCTGGGCAGTGGAATGTCAAATAAGATGTGGGACAGCCTTGTTGATCATGCAAAGACGTGTGTCTTAAGTGGAAAGCATTATGTATACTATGCTAGAG
||||||   |||| |  |  ||    ||| |     |  || | | |  | |      | ||    |   | ||||||| || ||||| ||||||||||||||||||||  |    || || ||||| || ||||| ||| | || |||||||  ||||| || |||||    |
gtaagta--atgaaagttagttt---tttctttctctctctctgtcagctcatgtagttggt---ctggcgcagATTCTTGGAAGTGGCATGTCAAATAAGATGTGGGAAGGAACAGTGGAGCATGCTAAAACGTGCGTCCTCAGCGGAAAGCTGTATGTCTATTATGCCGACG

upper sequence: GRMZM2G054109_T01 (Zea mays), 3'ss of exon 6
lower sequence: EFJ05811 (Selaginella moellendorffii), 3'ss of exon 5
gtaagttctatgataccttattgtgatttatggtatttcctatatgatttgacaccccttgttcttttt-tgtagATTCTGGGCAGTGGAATGTCAAATAAGATGTGGGACAGCCTTGTTGATCATGCAAAGACGTGTGTCTTAAGTGGAAAGCATTATGTATACTATGCTAGAG
||||||  |  | |   || |     |||       |  || | |  ||   | |   | |||  | |   | ||||||| || ||||| ||||||||||||||||||||  |    || || ||||| || ||||| ||| | || |||||||  ||||| || |||||    |
gtaagtaatgagtttttttctctctcttt------ctctctctttctttcagctcatgtagttggtctggcgcagATTCTTGGAAGTGGCATGTCAAATAAGATGTGGGAAGGAACAGTGGAGCATGCTAAAACGTGCGTCCTCAGCGGAAAGCTGTATGTCTATTATGCCGACG

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|211080472|gb|FK973121.1|FK973121
EST:     TTGTTAGGGATCAGCAGAGATTACGTAGC                         ATTCTGGGCAGTGGAATGTCAAATAAGATGTGGGACAGCCTTGTTGATCAT
genomic: TTGTTAGGGATCAGCAGAGATTACGTAGCgtaagttcta ... ttttttgtagATTCTGGGCAGTGGAATGTCAAATAAGATGTGGGACAGCCTTGTTGATCAT
EST: gi|211080474|gb|FK973123.1|FK973123
EST:     TTGAAGATTTCCTCCAGCTTCTTGTTAGGGATCAGCAGAGATTACGTAGC                         ATTCTGGGCAGTGGAATGTCAAATAAGATGTGGGACAGCCTTGTTGATCAT
genomic: TTGAAGATTTCCTCCAGCTTCTTGTTAGGGATCAGCAGAGATTACGTAGCgtaagttcta ... ttttttgtagATTCTGGGCAGTGGAATGTCAAATAAGATGTGGGACAGCCTTGTTGATCAT
EST: gi|211080473|gb|FK973122.1|FK973122
EST:     TTGTTAGGGATCAGCAGAGATTACGTAGC                         ATTCTGGGCAGTGGAATGTCAAATAAGATGTGGGACAGCCTTGTTGATCAT
genomic: TTGTTAGGGATCAGCAGAGATTACGTAGCgtaagttcta ... ttttttgtagATTCTGGGCAGTGGAATGTCAAATAAGATGTGGGACAGCCTTGTTGATCAT
EST: gi|211080475|gb|FK973124.1|FK973124
EST:     TTGTTAGGGATCAGCAGAGATTACGTAGC                         ATTCTGGGCAGTGGAATGTCAAATAAGATGTGGGACAGCCTTGTTGATCAT
genomic: TTGTTAGGGATCAGCAGAGATTACGTAGCgtaagttcta ... ttttttgtagATTCTGGGCAGTGGAATGTCAAATAAGATGTGGGACAGCCTTGTTGATCAT

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: 312

CAAGGATGGCGCATTCCACAAGAAGTTAAATGCTAGTGGGATCTATACAGTTGAAGATTTCCTCCAGCTTCTTGTTAGGGATCAGCAGAGATTACGTAGCgtaagttcta ... ttttttgtagATTCTGGGCAGTGGAATGTCAAATAAGATGTGGGACAGCCTTGTTGATCATGCAAAGACGTGTGTCTTAAGTGGAAAGCATTATGTATACTATGCTAGAG


Block sizes: 45 (upstream exon), 49 (downstream exon)
Score: 233

CAAGGATGGCGCATTCCACAAGAAGTTAAATGCTAGTGGGATCTATACAGTTGAAGATTTCCTCCAGCTTCTTGTTAGGGATCAGCAGAGATTACGTAGCgtaagttcta ... ttttttgtagATTCTGGGCAGTGGAATGTCAAATAAGATGTGGGACAGCCTTGTTGATCATGCAAAGACGTGTGTCTTAAGTGGAAAGCATTATGTATACTATGCTAGAG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 195

CAAGGATGGCGCATTCCACAAGAAGTTAAATGCTAGTGGGATCTATACAGTTGAAGATTTCCTCCAGCTTCTTGTTAGGGATCAGCAGAGATTACGTAGCgtaagttcta ... ttttttgtagATTCTGGGCAGTGGAATGTCAAATAAGATGTGGGACAGCCTTGTTGATCATGCAAAGACGTGTGTCTTAAGTGGAAAGCATTATGTATACTATGCTAGAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 162

CAAGGATGGCGCATTCCACAAGAAGTTAAATGCTAGTGGGATCTATACAGTTGAAGATTTCCTCCAGCTTCTTGTTAGGGATCAGCAGAGATTACGTAGCgtaagttcta ... ttttttgtagATTCTGGGCAGTGGAATGTCAAATAAGATGTGGGACAGCCTTGTTGATCATGCAAAGACGTGTGTCTTAAGTGGAAAGCATTATGTATACTATGCTAGAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

attgtgatttatggtatttcctatatgatttgacaccccttgttcttttttgtagATTCTGGGCAGTGGAATGTCAAATAAGATGTGGGACAGCCTTGTTGATCATGCAAAGACGTGTGTCTTAAGTGGAAAGCATTATGTATACTATGCTAGAG
                           atttgac  putative branch site (score: 162)
                                 caccccttgttctttt  CT-rich tract
                     tatatgattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagttctatgataccttattgtgatttatggtatttcctatatgatttgacaccccttgttcttttttgtagATTCTGGGCAGTGGAATGTCAAATAAGATGTGGGACAGCCTTGTTGATCATGCAAAGACGTGTGTCTTAAGTGGAAAGCATTATGTATACTATGCTAGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGTGGA