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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaggtcaataggcttttcctgttctgccatacattgggttatctcatctataaagccgcttctgtttgtcagGATATCAAGAGAAGTTTTATTTCAACCCCGGTGACACTGGCTTTAAG

Basic information

species Zea mays
transcript GRMZM2G073950_T01
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G073950_T01 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os02g33080.2 (Oryza sativa), 3'ss of exon 3
-----------gtaaggt---caataggcttttcctgttct-gccatacattgggttatctcatctataaagccgcttctgttt--gtcagGATATCAAGAGAAGTTTTATTTCAACCCCGGTGACACTGGCTTTAAG
           |||  ||     | ||  |     |   || | |||  | |   | || | | | |   |||   |||  |||  |  ||| ||||||||||| ||||||||||| || |||||||| ||||| |||
gtattgcccatgtatagtttatgacagattcactatagactagtcatggactatctgatttaaacaagttagctatttcctttttggctagGTTATCAAGAGAAATTTTATTTCAATCCTGGTGACACCGGCTTCAAG

upper sequence: GRMZM2G073950_T01 (Zea mays), 3'ss of exon 4
lower sequence: AT2G27450.2 (Arabidopsis thaliana), 3'ss of exon 4
gtaaggtcaataggcttttcctgttctgccatacattgg--gttatctcatctataaagccgcttctgtttgtcagGATATCAAGAGAAGTTTTATTTCAACCCCGGTGACACTGGCTTTAAG
|| ||   | |  |   ||     | |  | |   ||    |||| ||  |   | |  || ||| |  |  | ||| ||||||||||||||||||||||| || || || ||||||||||||
gtgagtcaagtttggagttggaaatatagcttgagtttcttgttacctttttgctgagacctctttttatcttaagGTTATCAAGAGAAGTTTTATTTCAATCCTGGAGATACTGGCTTTAAG

upper sequence: GRMZM2G073950_T01 (Zea mays), 3'ss of exon 4
lower sequence: EFJ07601 (Selaginella moellendorffii), 3'ss of exon 4
gtaaggtcaataggcttttcctgttctgccatacattgggttatctcatctataaagccgcttctgtttgtcagGATATCAAGAGAAGTTTTATTTCAACCCCGGTGACACTGGCTTTAAG
          || || |       | ||    |||     |  | |||||| |    |  ||| ||     ||||||||||||| |||||||||||||||||||| ||||| ||||| |||
---------gtatgcatgaatcaatttgtttcaca--aaatcgtttcatcttt----cgccttgtg-----cagGATATCAAGAAAAGTTTTATTTCAACCCCGGAGACACAGGCTTCAAG

upper sequence: GRMZM2G073950_T01 (Zea mays), 3'ss of exon 4
lower sequence: EFJ10979 (Selaginella moellendorffii), 3'ss of exon 4
gtaaggtcaataggcttttcctgttctgccatacattgggttatctcatctataaagccgcttctgtttgtcagGATATCAAGAGAAGTTTTATTTCAACCCCGGTGACACTGGCTTTAAG
          || || |       | ||    |||  |  |  | |||||| |    |  ||| ||     ||||||||||||| |||||||||||||||||||| ||||| ||||| |||
---------gtatgcatgaatcaatgtgtttcaca--gaatcgtttcatcttt----cgccttgtg-----cagGATATCAAGAAAAGTTTTATTTCAACCCCGGAGACACAGGCTTCAAG

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|211141687|gb|FL053515.1|FL053515
EST:     TGGCGCTGACCTTGGACTCTATCGCAAATCACACATTCCAGATGGACCAG                         GATACCAAGAGAAGTTTTATTTCAACCCCGGTGACACTGGCTTTAAG
genomic: TGGCGCTGATCTTGGACTCTATCGCAAATCACACATTCCAGATGGACCAGgtaaggtcaa ... tgtttgtcagGATATCAAGAGAAGTTTTATTTCAACCCCGGTGACACTGGCTTTAAG
EST: gi|78077685|gb|DV506119.1|DV506119
EST:     TGGCGCTGATCTTGGATTCTTTCGCAAATCACACATTCCAGATGGAGCAG                         GATATCAAGAGAAGTTTTATTTCAACCCCGGTGACACTGGCTTTAAG
genomic: TGGCGCTGATCTTGGACTCTATCGCAAATCACACATTCCAGATGGACCAGgtaaggtcaa ... tgtttgtcagGATATCAAGAGAAGTTTTATTTCAACCCCGGTGACACTGGCTTTAAG
EST: gi|211141683|gb|FL053511.1|FL053511
EST:     TGGCGCTGACCTTGGACTCTATCGCAAATCACACATTCCAGATGGACCAG                         GATACCAAGAGAAGTTTTATTTCAACCCCGGTGACACTGGCTTTAAG
genomic: TGGCGCTGATCTTGGACTCTATCGCAAATCACACATTCCAGATGGACCAGgtaaggtcaa ... tgtttgtcagGATATCAAGAGAAGTTTTATTTCAACCCCGGTGACACTGGCTTTAAG
EST: gi|113702021|gb|EE679525.1|EE679525
EST:     TGGCGTTGATCTTGGACTCTATCGCAAATCACACATTCCAGATGGACCAG                         GATATCAAGAGAAGTTTTATTTCAACCCCGGTGACACTGGCTTTAAG
genomic: TGGCGCTGATCTTGGACTCTATCGCAAATCACACATTCCAGATGGACCAGgtaaggtcaa ... tgtttgtcagGATATCAAGAGAAGTTTTATTTCAACCCCGGTGACACTGGCTTTAAG
EST: gi|29130437|gb|CB381141.1|CB381141
EST:     CTATCGCAAATCACACATTCCAGATGGACCAG                         GATATCAAGAGAAGTTTTATTTCAACCCCGGTGACACTGGCTTTAAG
genomic: CTATCGCAAATCACACATTCCAGATGGACCAGgtaaggtcaa ... tgtttgtcagGATATCAAGAGAAGTTTTATTTCAACCCCGGTGACACTGGCTTTAAG
EST: gi|91056600|gb|EB167018.1|EB167018
EST:     TGGCGCTGATCTTGGACTCTATCGCAAATCACACATTCCAGATGGACCAG                         GATATCAAGAGAAGTTTTATTTCAACCCCGGTGACACTGGCTTTAAG
genomic: TGGCGCTGATCTTGGACTCTATCGCAAATCACACATTCCAGATGGACCAGgtaaggtcaa ... tgtttgtcagGATATCAAGAGAAGTTTTATTTCAACCCCGGTGACACTGGCTTTAAG
EST: gi|148953399|gb|EE152896.2|EE152896
EST:     TGGCGCTGATCTTGGACTCTATCGCAAATCACACATTCCAGATGGACCAG                         GATATCAAGAGAAGTTTTATTTCAACCCCGGTGACACTGGCTTTAAG
genomic: TGGCGCTGATCTTGGACTCTATCGCAAATCACACATTCCAGATGGACCAGgtaaggtcaa ... tgtttgtcagGATATCAAGAGAAGTTTTATTTCAACCCCGGTGACACTGGCTTTAAG
EST: gi|78081735|gb|DV510147.1|DV510147
EST:     TGGCGCTGATCTTGGACTCTATCGCAAATCACACATTCCAGATGGACCAG                         GATATCAAGAGAAGTTTTATTTCAACCCCGGTGACACTGGCTTTAAG
genomic: TGGCGCTGATCTTGGACTCTATCGCAAATCACACATTCCAGATGGACCAGgtaaggtcaa ... tgtttgtcagGATATCAAGAGAAGTTTTATTTCAACCCCGGTGACACTGGCTTTAAG
EST: gi|88758160|gb|DY542301.1|DY542301
EST:     TGGCGCTGATCTTGGACTCTATCGCAAATCACACATTCCAGATGGACCAG                         GATATCAAGAGAAGTTTTATTTCAACCCCGGTGACACTGGCTTTAAG
genomic: TGGCGCTGATCTTGGACTCTATCGCAAATCACACATTCCAGATGGACCAGgtaaggtcaa ... tgtttgtcagGATATCAAGAGAAGTTTTATTTCAACCCCGGTGACACTGGCTTTAAG
EST: gi|50324199|gb|CO519325.1|CO519325
EST:     TGGCGCTGATCTTGGACTCTATCGCAAATCACACATTCCAGATGGACCAG                         GATATCAAGAGAAGTTTTATTTCAACCCCGGTGACACTGGCTTTAAG
genomic: TGGCGCTGATCTTGGACTCTATCGCAAATCACACATTCCAGATGGACCAGgtaaggtcaa ... tgtttgtcagGATATCAAGAGAAGTTTTATTTCAACCCCGGTGACACTGGCTTTAAG
EST: gi|84908437|gb|DW404315.1|DW404315
EST:     TGGCGCTGACCTTGGACTCTATCGCAAATCACACATTCCAGATGGACCAG                         GATACCAAGAGAAGTTTTATTTCAACCCCGGTGACACTGGCTTTAAG
genomic: TGGCGCTGATCTTGGACTCTATCGCAAATCACACATTCCAGATGGACCAGgtaaggtcaa ... tgtttgtcagGATATCAAGAGAAGTTTTATTTCAACCCCGGTGACACTGGCTTTAAG
EST: gi|60346678|gb|DN213651.1|DN213651
EST:     TGGCGCTGATCTTGGACTCTATCGCAAATCACACATTCCAGATGGACCAG                         GATATCAAGAGAAGTTTTATTTCAACCCCGGTGACACTGGCTTTAAG
genomic: TGGCGCTGATCTTGGACTCTATCGCAAATCACACATTCCAGATGGACCAGgtaaggtcaa ... tgtttgtcagGATATCAAGAGAAGTTTTATTTCAACCCCGGTGACACTGGCTTTAAG
EST: gi|148939361|gb|EC883888.2|EC883888
EST:     TGGCGCTGATCTTGGACTCTATCGCAAATCACACATTCCAGATGGACCAG                         GATATCAAGAGAAGTTTTATTTCAACCCCGGTGACACTGGCTTTAAG
genomic: TGGCGCTGATCTTGGACTCTATCGCAAATCACACATTCCAGATGGACCAGgtaaggtcaa ... tgtttgtcagGATATCAAGAGAAGTTTTATTTCAACCCCGGTGACACTGGCTTTAAG
EST: gi|78078908|gb|DV507320.1|DV507320
EST:     TGGCGCTGATCTTGGACTCTATCGCAAATCACACATTCCAGATGGACCAG                         GATATCAAGAGAAGTTTTATTTCAACCCCGGTGACACTGGCTTTAAG
genomic: TGGCGCTGATCTTGGACTCTATCGCAAATCACACATTCCAGATGGACCAGgtaaggtcaa ... tgtttgtcagGATATCAAGAGAAGTTTTATTTCAACCCCGGTGACACTGGCTTTAAG
EST: gi|71417126|gb|DR803932.1|DR803932
EST:     ATTCCAGATGGACCAG                         GATATCAAGAGAAGTTTTATTTCAACCCCGGTGACACTGGCTTTAAG
genomic: ATTCCAGATGGACCAGgtaaggtcaa ... tgtttgtcagGATATCAAGAGAAGTTTTATTTCAACCCCGGTGACACTGGCTTTAAG
EST: gi|71417127|gb|DR803933.1|DR803933
EST:     TGGCGCTGATCTTGGACTCTATCGCAAATCACACATTCCAGATGGACCAG                         GATATCAAGAGAAGTTTTATTTCAACCCCGGTGACACTGGCTTTAAG
genomic: TGGCGCTGATCTTGGACTCTATCGCAAATCACACATTCCAGATGGACCAGgtaaggtcaa ... tgtttgtcagGATATCAAGAGAAGTTTTATTTCAACCCCGGTGACACTGGCTTTAAG
EST: gi|94478259|gb|EB707217.1|EB707217
EST:     TGGCGCTGATCTTGGACTCTATCGCAAATCACACATTCCAGATGGACCAG                         GATATCAAGAGAAGTTTTATTTCAACCCCGGTGACACTGGCTTTAAG
genomic: TGGCGCTGATCTTGGACTCTATCGCAAATCACACATTCCAGATGGACCAGgtaaggtcaa ... tgtttgtcagGATATCAAGAGAAGTTTTATTTCAACCCCGGTGACACTGGCTTTAAG
EST: gi|78077686|gb|DV506120.1|DV506120
EST:     TGGCGCTGATCTTGGACTCTATCGCAAATCACACATTCCAGATGGACCAG                         GATATCAAGAGAAGTTTTATTTCAACCCCGGTGACACTGGCTTTAAG
genomic: TGGCGCTGATCTTGGACTCTATCGCAAATCACACATTCCAGATGGACCAGgtaaggtcaa ... tgtttgtcagGATATCAAGAGAAGTTTTATTTCAACCCCGGTGACACTGGCTTTAAG

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: 49 (upstream exon), 47 (downstream exon)
Score: 210

GAAGAAGCAAACAATGCACATTATAATTCGGTGGCTATTATCGATGCTGATGGCGCTGATCTTGGACTCTATCGCAAATCACACATTCCAGATGGACCAGgtaaggtcaa ... tgtttgtcagGATATCAAGAGAAGTTTTATTTCAACCCCGGTGACACTGGCTTTAAG


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 314

GAAGAAGCAAACAATGCACATTATAATTCGGTGGCTATTATCGATGCTGATGGCGCTGATCTTGGACTCTATCGCAAATCACACATTCCAGATGGACCAGgtaaggtcaa ... tgtttgtcagGATATCAAGAGAAGTTTTATTTCAACCCCGGTGACACTGGCTTTAAG


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 305

GAAGAAGCAAACAATGCACATTATAATTCGGTGGCTATTATCGATGCTGATGGCGCTGATCTTGGACTCTATCGCAAATCACACATTCCAGATGGACCAGgtaaggtcaa ... tgtttgtcagGATATCAAGAGAAGTTTTATTTCAACCCCGGTGACACTGGCTTTAAG


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 355

GAAGAAGCAAACAATGCACATTATAATTCGGTGGCTATTATCGATGCTGATGGCGCTGATCTTGGACTCTATCGCAAATCACACATTCCAGATGGACCAGgtaaggtcaa ... tgtttgtcagGATATCAAGAGAAGTTTTATTTCAACCCCGGTGACACTGGCTTTAAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cctgttctgccatacattgggttatctcatctataaagccgcttctgtttgtcagGATATCAAGAGAAGTTTTATTTCAACCCCGGTGACACTGGCTTTAAG
                                         cttctgttt  CT-rich tract
                            atctataaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaaggtcaataggcttttcctgttctgccatacattgggttatctcatctataaagccgcttctgtttgtcagGATATCAAGAGAAGTTTTATTTCAACCCCGGTGACACTGGCTTTAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGT