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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tttgagcttcttaggacttgctcttcctttctggagaaactccctcttttagcctctgctgggccatccaagctaatttacttgttcactgtatcttcagGCTTGCGACATCAAAGATCCAAAGCAGAACATCGAGTGGACAGTTCCAGAAGGTGGAGGTGGTCCTGGTTACACAGTAATGTAGAATGCTCAATGATGAA

Basic information

species Zea mays
transcript GRMZM2G032222_T02
intron # 17
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G032222_T02 (Zea mays), 3'ss of exon 17
lower sequence: LOC_Os10g37210.1 (Oryza sativa), 3'ss of exon 17
tttgagcttcttaggacttgctcttcctttctggagaaactccctcttttagcctctgctgggccatccaagctaatttacttgttcactgtatcttcagGCTTGCGACATCAAAGATCCAAAGCAGAACATCGAGTGGACAGTTCCAGAAGGTGGAGGTGGTCCTGGTTACACAGTAATGTAGAATGCTCAATGATGAA
| | | | ||| | | || || | | | ||| | || | | || | | | |||| || |||||| |||||||| |||||||||||||||||||| |||||||| ||||| ||||||||||||||||| ||||| || |||||||||||||||| | ||
--gtatttgcctccatgttgattcagttgtccatggacatttgcatcttttgtttcctgt----------aactgaatgaaatgttgacggtatctgcagGCTTGTGACATCAAAGATCCAAAGCAAAACATCGAATGGACCGTTCCAGAAGGTGGAGGCGGTCCAGGGTACACAGTAATGTAGACGATAGCAAAATACT

upper sequence: GRMZM2G032222_T02 (Zea mays), 3'ss of exon 17
lower sequence: GLYMA15G03360.1 (Glycine max), 3'ss of exon 17
-tttgagcttcttaggacttgctcttcctttctggagaaactccctctttta--gcctctgctgggccatccaagctaatttac--ttgttcactgtatcttcagGCTTGCGACATCAAAGATCCAAAGCAGAACATCGAGTGGACAGTTCCAGAAGGTGGAGGTGGTCCTGGTTACACAGTAATGTAGAATGCTCAATGATGAA
| || | | | |||||| | | | || | || || | || || | | | || ||||| || ||||||| | | ||||||||| || ||||||||||||||||| || || ||||||||||| || ||||| || || || || || ||| |||| |||||| | || | |
ccattaggatgcaatgtcttgcttctttaataatactatacctacactagtaaagtctttgtttc-ctacccggtttaattcacacttgttcattat----tcagGCTTGTGATATCAAAGATCCAAAGCAAAATATTGAGTGGACAGTGCCTGAAGGGGGTGGAGGCCCAGGATACTCAGTCATGTAGTCATGGTATTGTTCAC

upper sequence: GRMZM2G032222_T02 (Zea mays), 3'ss of exon 17
lower sequence: AT2G43400.1 (Arabidopsis thaliana), 3'ss of exon 17
-tttgagcttcttag-gacttgctcttcctt-tctggagaaactccctcttttagcctctgctgggccat--------ccaagctaatttacttgttcactgtatcttca--gGCTTGCGACATCAAAGATCCAAAGCAGAACATCGAGTGGACAGTTCCAGAAGGTGGAGGTGGTCCTGGTTACACAGTAATGTAGAATGCTCAATGATGAA--
| | ||| |||||| | | || | | | | | | | | | | | | | || | ||| ||| || | || | | ||| || |||||||||||||||||||||||||| ||||||||||| || |||||||| || || |||| || | | |||||| | || || | ||
gtacgcatcacttgtcgacttgatgcactttgtgttaaagtatgtctattcatgtcattcgattgattttggagaagcttaaattggttttctttttttttttaatctaaaagGCATGTGACATCAAAGATCCAAAGCAGAACATAGAGTGGACAGTGCCTGAAGGTGGTGGAGGCCCTGCCTATTCCCTCATGTAG--TCCTTAAGATTCAACA

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|78120295|gb|DV538679.1|DV538679
EST:     AAGGTGACCCAAAGCTTCATATAAATGCACAGAATTGTTTTCATTGCAAG                         GCTTGCGACATCAAAGATCCAAAGCAGAACATCGAGTGGACAGTTCCAGAA
genomic: AAGGTGACCCAAAGCTTCATATAAATGCACAGAATTGTCTTCATTGCAAGgtaaactttt ... gtatcttcagGCTTGCGACATCAAAGATCCAAAGCAGAACATCGAGTGGACAGTTCCAGAA
EST: gi|94479206|gb|EB708164.1|EB708164
EST:     AAGGTGACCCAAAGCTTCATATAAATGCACAGAATTGTTTTCATTGCAAG                         GCTTGCGACATCAAAGATCCAAAGCAGAACATCGAGTGGACAGTTCCAGAA
genomic: AAGGTGACCCAAAGCTTCATATAAATGCACAGAATTGTCTTCATTGCAAGgtaaactttt ... gtatcttcagGCTTGCGACATCAAAGATCCAAAGCAGAACATCGAGTGGACAGTTCCAGAA
EST: gi|71756373|gb|DR954310.1|DR954310
EST:     AAGGTGACCCAAAGCTTCATATAAATGCACAGAATTGTTTTCATTGCAAG                         GCTTGCGACATCAAAGATCCAAAGCAGAACATCGAGTGGACAGTTCCAGAA
genomic: AAGGTGACCCAAAGCTTCATATAAATGCACAGAATTGTCTTCATTGCAAGgtaaactttt ... gtatcttcagGCTTGCGACATCAAAGATCCAAAGCAGAACATCGAGTGGACAGTTCCAGAA
EST: gi|87157160|gb|DY401949.1|DY401949
EST:     AAGGTGACCCAAAGCTTCATATAAATGCACAGAATTGTCTTCATTGCAAG                         GCTTGCGACATCAAAGATCCAAAGCAGAACATCGAGTGGACAGTTCCAGAA
genomic: AAGGTGACCCAAAGCTTCATATAAATGCACAGAATTGTCTTCATTGCAAGgtaaactttt ... gtatcttcagGCTTGCGACATCAAAGATCCAAAGCAGAACATCGAGTGGACAGTTCCAGAA
EST: gi|161593692|gb|EY964319.1|EY964319
EST:     AGGTGACCCAAAGCTTCATATAAATGCACAGAATTGTCTTCAATTGCAAG                         GCTTGCGACATCAAAG
genomic: AGGTGACCCAAAGCTTCATATAAATGCACAGAATTGTCTTCA-TTGCAAGgtaaactttt ... gtatcttcagGCTTGCGACATCAAAG
EST: gi|31353246|gb|CD437603.1|CD437603
EST:     AAGGTGACCCAAAGCTTCATATAAATGCACAGAATTGTCTTCATTGCAAG                         GCTTGCGACATCAAAGATCCAAAGCAGAACATCGAGTGGACAGTTCCAGAA
genomic: AAGGTGACCCAAAGCTTCATATAAATGCACAGAATTGTCTTCATTGCAAGgtaaactttt ... gtatcttcagGCTTGCGACATCAAAGATCCAAAGCAGAACATCGAGTGGACAGTTCCAGAA
EST: gi|76020278|gb|DT947448.1|DT947448
EST:     AAGGTGACCCAAAGCTTCATATAAATGCACAGAATTGTCTTCATTGCAAG                         GCTTGCGACATCAAAGATCCAAAGCAGAACATCGAGTGGACAGTTCCAGAA
genomic: AAGGTGACCCAAAGCTTCATATAAATGCACAGAATTGTCTTCATTGCAAGgtaaactttt ... gtatcttcagGCTTGCGACATCAAAGATCCAAAGCAGAACATCGAGTGGACAGTTCCAGAA
EST: gi|24773594|gb|CA408848.1|CA408848
EST:     AAGGTGACCCAAAGCTTCATATAAATGCACAGAATTGTCTTCATTGCAAG                         GCGTTGCGACATCAAAGATCCAAAGCAGAACATCGAGTGGACAGTTCCAGA
genomic: AAGGTGACCCAAAGCTTCATATAAATGCACAGAATTGTCTTCATTGCAAGgtaaactttt ... gtatcttcagGC-TTGCGACATCAAAGATCCAAAGCAGAACATCGAGTGGACAGTTCCAGA
EST: gi|21809980|gb|BQ668298.1|BQ668298
EST:     AAGGTGACCCAAAGCTTCATATAAATGCACAGAATTGTCTTCATTGCAAG                         GCTTGCGACATCAAAGATCCAAAGCAGAACATCGAGTGGACAGTTCCAGAA
genomic: AAGGTGACCCAAAGCTTCATATAAATGCACAGAATTGTCTTCATTGCAAGgtaaactttt ... gtatcttcagGCTTGCGACATCAAAGATCCAAAGCAGAACATCGAGTGGACAGTTCCAGAA

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), 48 (downstream exon)
Score: 26

ATATATCTCTGATGAGAAAGGTGACCCAAAGCTTCATATAAATGCACAGAATTGTCTTCATTGCAAGgtaaactttt ... gtatcttcagGCTTGCGACATCAAAGATCCAAAGCAGAACATCGAGTGGACAGTTCCAGAAGGTGGAGGTGGTCCTGGTTACACAGTAATGTAGAATGCTCAATGATGAA


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 84

ATATATCTCTGATGAGAAAGGTGACCCAAAGCTTCATATAAATGCACAGAATTGTCTTCATTGCAAGgtaaactttt ... gtatcttcagGCTTGCGACATCAAAGATCCAAAGCAGAACATCGAGTGGACAGTTCCAGAAGGTGGAGGTGGTCCTGGTTACACAGTAATGTAGAATGCTCAATGATGAA


Block sizes: 47 (upstream exon), 48 (downstream exon)
Score: 56

ATATATCTCTGATGAGAAAGGTGACCCAAAGCTTCATATAAATGCACAGAATTGTCTTCATTGCAAGgtaaactttt ... gtatcttcagGCTTGCGACATCAAAGATCCAAAGCAGAACATCGAGTGGACAGTTCCAGAAGGTGGAGGTGGTCCTGGTTACACAGTAATGTAGAATGCTCAATGATGAA


Block sizes: 48 (upstream exon), 48 (downstream exon)
Score: 55

ATATATCTCTGATGAGAAAGGTGACCCAAAGCTTCATATAAATGCACAGAATTGTCTTCATTGCAAGgtaaactttt ... gtatcttcagGCTTGCGACATCAAAGATCCAAAGCAGAACATCGAGTGGACAGTTCCAGAAGGTGGAGGTGGTCCTGGTTACACAGTAATGTAGAATGCTCAATGATGAA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cttttagcctctgctgggccatccaagctaatttacttgttcactgtatcttcagGCTTGCGACATCAAAGATCCAAAGCAGAACATCGAGTGGACAGTTCCAGAAGGTGGAGGTGGTCCTGGTTACACAGTAATGTAGAATGCTCAATGATGAA
                         agctaat  putative branch site (score: 55)
 tatcttc  putative PPT
 taatttactt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tttgagcttcttaggacttgctcttcctttctggagaaactccctcttttagcctctgctgggccatccaagctaatttacttgttcactgtatcttcagGCTTGCGACATCAAAGATCCAAAGCAGAACATCGAGTGGACAGTTCCAGAAGGTGGAGGTGGTCCTGGTTACACAGTAATGTAGAATGCTCAATGATGAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGG
- - agcttct
- - - - - - - - cttgctc
- - - - - - - - - - - - - ctttctg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gccatcc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ttacttg