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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaggacaatgacatgaacactcttcttcttcttccctagctagctttaagcaccatttaaattctattcatcaaggtcatgtctgaatgtttggatattttgaactgtggttgatcagCTTCTTCAAGGAGTGTCCACACCCGGATGACAAGCAGCGAAAGGAGCTGAGCCGGGAGCTCGGTCTCGAGCCGCTGCAGGTCAAGTTCTGGTTCCAGAAC

Basic information

species Zea mays
transcript GRMZM2G118063_T02
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G118063_T03 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os08g08820.1 (Oryza sativa), 3'ss of exon 3
---------------------------gtaaggacaatgacatgaacactcttcttcttctt-----ccctagctagctttaagcaccatt-taaattctattcatcaaggtcatgtctgaatgtttggatattttgaactgtggttgatcagCTTCTTCAAGGAGTGTCCACACCCGGATGACAAGCAGCGAAAGGAGCTGAGCCGGGAGCTCGGTCTCGAGCCGCTGCAGGTCAAGTTCTGGTTCCAGAAC
                            |     ||||     ||  | | |  |    |||      | | |  || || |   |   || | ||| |||||||||| | | || | || |  ||  |  | | |         |||||||| |||||||||||||| || ||||| || ||||||||||| |||||||||||| ||||||| ||||| || || |||||||| || |||||||| ||||||
gtaagattaatttatcatttcatccctatgttttcaattctgagataattttcttctcccttgcaaatctttgtcagattgattaaatgttatgaatcctattcatca-gttgatctttgtagattaagtaaatgtttgtgaattttgatcagTTTCTTCAAGGAGTGCCCGCACCCAGACGACAAGCAGCGCAAGGAGCTGAGCAGGGAGCTGGGTCTTGAACCTCTGCAGGTTAAATTCTGGTTTCAGAAC

upper sequence: GRMZM2G118063_T03 (Zea mays), 3'ss of exon 3
lower sequence: EFJ37532 (Selaginella moellendorffii), 3'ss of exon 1
gtaaggacaatgacatgaacactcttcttcttcttccctagctagctttaagcaccatttaaattctattcatcaaggtcatgtctgaatgtttggatattttgaactgtggttgatcagCTTCTTCAAGGAGTGTCCACACCCGGATGACAAGCAGCGAAAGGAGCTGAGCCGGGAGCTCGGTCTCGAGCCGCTGCAGGTCAAGTTCTGGTTCCAGAAC
                                                           ||| | ||      | ||  ||||  |||    ||   | | ||     |||      ||| || |||||||||||||| || || || || ||||||||  ||||||||||||||||||| || || ||||| | ||| |||||||||||||||||||| 
----------------------------------------------------------gtaagtactgcaagccgagagcatga-tgagaacttatctttctt----cgtg-----ccagGTTGTTCAAGGAGTGTCCTCATCCCGACGATAAGCAGCGCCAGGAGCTGAGCCGGGAGCTAGGACTGGAGCCTCGGCAAGTCAAGTTCTGGTTCCAGAAT

upper sequence: GRMZM2G118063_T03 (Zea mays), 3'ss of exon 3
lower sequence: EFJ10492 (Selaginella moellendorffii), 3'ss of exon 2
gtaaggacaatgacatgaacactcttcttcttcttccctagctagctttaagcaccatttaaattctattcatcaaggtcatgtctgaatgtttggatattttgaactgtggttgatcagCTTCTTCAAGGAGTGTCCACACCCGGATGACAAGCAGCGAAAGGAGCTGAGCCGGGAGCTCGGTCTCGAGCCGCTGCAGGTCAAGTTCTGGTTCCAGAAC
                                              |   ||     |||   |  | ||| || |    | |||   | | | |  | |||     | |  | |  |||||| ||||||||||| || || |||||||||||||||||  ||||||| ||||||||||||||  | ||||||| ||| |||||||| ||||||||||| 
---------------------------------------------gtaagagattggttttggtgttgttc-tcgattggaagtcctcaaggtggattttttcttcgttttctcgcgcagCTTGTTCAAGGAGTGCCCGCATCCGGATGACAAGCAGCGGCAGGAGCTCAGCCGGGAGCTCGGATTGGAGCCGCGGCAAGTCAAGTTTTGGTTCCAGAAT

upper sequence: GRMZM2G118063_T03 (Zea mays), 3'ss of exon 3
lower sequence: EFJ34024 (Selaginella moellendorffii), 3'ss of exon 1
gtaaggacaatgacatgaacactcttcttcttcttccctagctagctttaagcaccatttaaattctattcatcaaggtcatgtctgaatgtttggatattttgaactgtggttgatcagCTTCTTCAAGGAGTGTCCACACCCGGATGACAAGCAGCGAAAGGAGCTGAGCCGGGAGCTCGGTCTCGAGCCGCTGCAGGTCAAGTTCTGGTTCCAGAAC
                                                           ||| | |||     | ||  ||||  |||    ||   | | ||     |||      ||| || |||||||||||||| || || || || ||||||||  ||||||||||||||||||| || || ||||| | ||| |||||||||||||||||||| 
----------------------------------------------------------gtaagtactacaagccgagagcatga-tgagaacttatctttctt----cgtg-----ccagGTTGTTCAAGGAGTGTCCTCATCCCGACGATAAGCAGCGCCAGGAGCTGAGCCGGGAGCTAGGACTGGAGCCTCGGCAAGTCAAGTTCTGGTTCCAGAAT

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|50335761|gb|CO530887.1|CO530887
EST:     AAGAAGCGGTATCACCGCCACACCCAGCACCAGATCGAAGAGATGGAGGC                         CTTCTTCAAGGAGTGTCCACACCCGGATGACAAGCAGCGAAAGGAGCTGAG
genomic: AAGAAGCGGTATCACCGCCACACCCAGCACCAGATCGAAGAGATGGAGGCgtaaggacaa ... ggttgatcagCTTCTTCAAGGAGTGTCCACACCCGGATGACAAGCAGCGAAAGGAGCTGAG
EST: gi|78087580|gb|DV515973.1|DV515973
EST:     AAGAAGCGGTATCACCGCCACACCCAGCACCAGATCGAAGAGATGGAGGC                         CTTCTTNCA-GGAGTGTCCACACCCGGATGACAAGCAGCGAAAGGAGCTGA
genomic: AAGAAGCGGTATCACCGCCACACCCAGCACCAGATCGAAGAGATGGAGGCgtaaggacaa ... ggttgatcagCTTCTT-CAAGGAGTGTCCACACCCGGATGACAAGCAGCGAAAGGAGCTGA
EST: gi|149100689|gb|EE186778.2|EE186778
EST:     AAGAAGCGGTATCACCGCCACACCCAGCACCAGATCGAAGAGATGGAGGC                         CTTCTTCAAGGAGTGTCCACACCCGGATGACAAGCAGCGAAAGGAGCTGAG
genomic: AAGAAGCGGTATCACCGCCACACCCAGCACCAGATCGAAGAGATGGAGGCgtaaggacaa ... ggttgatcagCTTCTTCAAGGAGTGTCCACACCCGGATGACAAGCAGCGAAAGGAGCTGAG
EST: gi|50323259|gb|CO518385.1|CO518385
EST:     AAGAAGCGGTATCACCGCCACACCCAGCACCAGATCGAAGAGATGGAGGC                         CTTCTTCAAGGAGTGTCCACACCCGGATGACAAGCAGCGAAAGGAGCTGAG
genomic: AAGAAGCGGTATCACCGCCACACCCAGCACCAGATCGAAGAGATGGAGGCgtaaggacaa ... ggttgatcagCTTCTTCAAGGAGTGTCCACACCCGGATGACAAGCAGCGAAAGGAGCTGAG
EST: gi|71767000|gb|DR964937.1|DR964937
EST:     AAGAAGCGGTATCACCGCCACACCCAGCACCAGATCGAAGAGATGGAGGC                         CTTCTTCAAGGAGTGTCCACACCCGGATGACAAGCAGCGAAAGGAGCTGAG
genomic: AAGAAGCGGTATCACCGCCACACCCAGCACCAGATCGAAGAGATGGAGGCgtaaggacaa ... ggttgatcagCTTCTTCAAGGAGTGTCCACACCCGGATGACAAGCAGCGAAAGGAGCTGAG
EST: gi|71299781|gb|DR785898.1|DR785898
EST:     AAGAAGCGGTATCACCGCCACACCCAGCACCAGATCGAAGAGATGGAGGC                         CTTCTTCAAGGAGTGTCCACACCCGGATGACAAGCAGCGAAAGGAGCTGAG
genomic: AAGAAGCGGTATCACCGCCACACCCAGCACCAGATCGAAGAGATGGAGGCgtaaggacaa ... ggttgatcagCTTCTTCAAGGAGTGTCCACACCCGGATGACAAGCAGCGAAAGGAGCTGAG
EST: gi|149102070|gb|EE287534.2|EE287534
EST:     AAGAAGCGGTATCACCGCCACACCCAGCACCAGATCGAAGAGATGGAGGC                         CTTCTTCAAGGAGTGTCCACACCCGGATGACAAGCAGCGAAAGGAGCTGAG
genomic: AAGAAGCGGTATCACCGCCACACCCAGCACCAGATCGAAGAGATGGAGGCgtaaggacaa ... ggttgatcagCTTCTTCAAGGAGTGTCCACACCCGGATGACAAGCAGCGAAAGGAGCTGAG
EST: gi|149015319|gb|EE045135.2|EE045135
EST:     AAGAAGCGGTATCACCGCCACACCCAGCACCAGATCGAAGAGATGGAGGC                         CTTCTTCAAGGAGTGTCCACACCCGGATGACAAGCAGCGAAAGGAGCTGAG
genomic: AAGAAGCGGTATCACCGCCACACCCAGCACCAGATCGAAGAGATGGAGGCgtaaggacaa ... ggttgatcagCTTCTTCAAGGAGTGTCCACACCCGGATGACAAGCAGCGAAAGGAGCTGAG
EST: gi|148953688|gb|EC899049.2|EC899049
EST:     AAGAAGCGGTATCACCGCCACACCCAGCACCAGATCGAAGAGATGGAGGC                         CTTCTTCAAGGAGTGTCCACACCCGGATGACAAGCAGCGAAAGGAGCTGAG
genomic: AAGAAGCGGTATCACCGCCACACCCAGCACCAGATCGAAGAGATGGAGGCgtaaggacaa ... ggttgatcagCTTCTTCAAGGAGTGTCCACACCCGGATGACAAGCAGCGAAAGGAGCTGAG
EST: gi|148934302|gb|EC878328.2|EC878328
EST:     AAGAAGCGGTATCACCGCCACACCCAGCACCAGATCGAAGAGATGGAGGC                         CTTCTTCAAGGAGTGTCCACACCCGGATGACAAGCAGCGAAAGGAGCTGAG
genomic: AAGAAGCGGTATCACCGCCACACCCAGCACCAGATCGAAGAGATGGAGGCgtaaggacaa ... ggttgatcagCTTCTTCAAGGAGTGTCCACACCCGGATGACAAGCAGCGAAAGGAGCTGAG

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 3 RNA-Seq libraries.


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 134

CCGGCGATGATGGCCAGGGGGACGAGGACCCTAACCAGCGGCCAAACAAGAAGAAGCGGTATCACCGCCACACCCAGCACCAGATCGAAGAGATGGAGGCgtaaggacaa ... ggttgatcagCTTCTTCAAGGAGTGTCCACACCCGGATGACAAGCAGCGAAAGGAGCTGAGCCGGGAGCTCGGTCTCGAGCCGCTGCAGGTCAAGTTCTGGTTCCAGAAC


Block sizes: 33 (upstream exon), 49 (downstream exon)
Score: 28

CCGGCGATGATGGCCAGGGGGACGAGGACCCTAACCAGCGGCCAAACAAGAAGAAGCGGTATCACCGCCACACCCAGCACCAGATCGAAGAGATGGAGGCgtaaggacaa ... ggttgatcagCTTCTTCAAGGAGTGTCCACACCCGGATGACAAGCAGCGAAAGGAGCTGAGCCGGGAGCTCGGTCTCGAGCCGCTGCAGGTCAAGTTCTGGTTCCAGAAC


Block sizes: 46 (upstream exon), 49 (downstream exon)
Score: 53

CCGGCGATGATGGCCAGGGGGACGAGGACCCTAACCAGCGGCCAAACAAGAAGAAGCGGTATCACCGCCACACCCAGCACCAGATCGAAGAGATGGAGGCgtaaggacaa ... ggttgatcagCTTCTTCAAGGAGTGTCCACACCCGGATGACAAGCAGCGAAAGGAGCTGAGCCGGGAGCTCGGTCTCGAGCCGCTGCAGGTCAAGTTCTGGTTCCAGAAC




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctattcatcaaggtcatgtctgaatgtttggatattttgaactgtggttgatcagCTTCTTCAAGGAGTGTCCACACCCGGATGACAAGCAGCGAAAGGAGCTGAGCCGGGAGCTCGGTCTCGAGCCGCTGCAGGTCAAGTTCTGGTTCCAGAAC
                               atattttgaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaaggacaatgacatgaacactcttcttcttcttccctagctagctttaagcaccatttaaattctattcatcaaggtcatgtctgaatgtttggatattttgaactgtggttgatcagCTTCTTCAAGGAGTGTCCACACCCGGATGACAAGCAGCGAAAGGAGCTGAGCCGGGAGCTCGGTCTCGAGCCGCTGCAGGTCAAGTTCTGGTTCCAGAAC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGCAG