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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgaatacataatatttattgttgtgaatttcttttcttgaacctgtttgtaataattgaggtttatgtgttgatgattgtagCCTGAGGACTGGGATGACAAGGAATACATTCCTGACCCTGAGGACAAGAAGCCAGAG

Basic information

species Zea mays
transcript GRMZM2G074687_T01
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G074687_T01 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os07g14270.2 (Oryza sativa), 3'ss of exon 4
gtgaat-acataatatttattgttgtgaatttcttttcttgaacctgtttgtaataattgaggtttatgtgttgatgattgtagCCTGAGGACTGGGATGACAAGGAATACATTCCTGACCCTGAGGACAAGAAGCCAGAG
||   |  |||| |  |   | |  || | | | || |||     | | |  |||  || || |  ||    | ||||||  |||| |||||||||||||||||||| ||||||||||||||||||||||||||||| |||
gtattttgcatattcctagctttcttggaatgccttgcttttgtgtctcttgaatg-ttaagat--attaccttatgattacagCCAGAGGACTGGGATGACAAGGAGTACATTCCTGACCCTGAGGACAAGAAGCCTGAG

upper sequence: GRMZM2G074687_T01 (Zea mays), 3'ss of exon 4
lower sequence: GLYMA10G28890.1 (Glycine max), 3'ss of exon 4
------gtgaatacataatatttatt--gttgtgaatttcttttcttgaacctgtttgtaataattgaggtttatgtgttgatgattgtagCCTGAGGACTGGGATGACAAGGAATACATTCCTGACCCTGAGGACAAGAAGCCAGAG
       |     || | |  |  ||   |||| |  ||   || | |   | ||||  |  | ||    | | |      ||  |   |||| || || ||||||||||| ||||| |||||||| |||||||| ||||| ||||||
gtacttttcttcccagagttgtagtttaattgtcagatttggttttggtttcggttttgatcatttctaatctttaat---atactcacagCCAGAAGATTGGGATGACAAAGAATATATTCCTGATCCTGAGGATAAGAAACCAGAG

upper sequence: GRMZM2G074687_T01 (Zea mays), 3'ss of exon 4
lower sequence: AT1G09210.1 (Arabidopsis thaliana), 3'ss of exon 4
---------------------------------------------------------------------------gtgaatacata--atattta----ttgttgtgaatttcttttcttgaacctg--------tttgtaata-attgaggtttatgtgttgatgattgtagCCTGAGGACTGGGATGACAAGGAATACATTCCTGACCCTGAGGACAAGAAGCCAGAG-------------------------------------------
                                                                            | |  ||| |  |||   |     | |  |||| ||  ||  ||  |||||        |   | ||| |    | |   | | || ||   |  |||||||||||||||| ||  | ||||||||| |||||||||| |||||||| || ||                                            
gtattctatttcttatgaacaaccaggctaaactgagaaccaaccacttatactcaattttggagcaaactagaactaaccacaaaccataccaaagctctctgatgaacttggttgattatacctgagataccatccatcatacaaattgatccttttatttatttgtacagCCTGAGGACTGGGACGAACAAGAATACATTTCTGACCCTGAAGACAAGAAACCTGACGGTTACGATGATATCCCTAAGGAGATCCCAGACACCGACTCAA

upper sequence: GRMZM2G074687_T01 (Zea mays), 3'ss of exon 4
lower sequence: Vv14s0060g01290.t01 (Vitis vinifera), 3'ss of exon 4
gtgaatacata-atatttattgttgtgaatttcttttc--ttgaacctgtttgtaataattgaggttt--atgtgttgatgattgtagCCTGAGGACTGGGATGACAAGGAATACATTCCTGACCCTGAGGACAAGAAGCCAGAG
|| | ||| ||   ||  |||      | ||||||||    | |||   |||   || |   |   |   || |  | |||||   ||||||| || |||||||| ||||| ||||||||||| ||||| ||  |||||||||||
gtaattacttatgcatcaattcagtccagtttctttttaacttaactaattttggatgaacaataatgcgattttataatgataacagCCTGAAGATTGGGATGAGAAGGAGTACATTCCTGATCCTGAAGATGAGAAGCCAGAG

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|148948737|gb|EC898659.2|EC898659
EST:     ACTGGGATATTCTTCCCCCTAAGCAAATCAAGGACCCAGAGGCTAAGAAG                         CCTGAGGACTGGGATGACAAGGAATACATTCCTGACCCTGAGGACAAGAAG
genomic: ACTGGGATATTCTTCCCCCTAAGCAAATCAAGGACCCAGAGGCTAAGAAGgtgaatacat ... atgattgtagCCTGAGGACTGGGATGACAAGGAATACATTCCTGACCCTGAGGACAAGAAG
EST: gi|211279487|gb|FL438453.1|FL438453
EST:     ACTGGGATATTCTTCCCCCTAAGCAAATCAAGGCCCCAGAGGCTAAGAAG                         CCTGAGGACTGGGATGACAAGGAATACATTCCTGACCCTGAGGACAAGAAG
genomic: ACTGGGATATTCTTCCCCCTAAGCAAATCAAGGACCCAGAGGCTAAGAAGgtgaatacat ... atgattgtagCCTGAGGACTGGGATGACAAGGAATACATTCCTGACCCTGAGGACAAGAAG
EST: gi|32846103|gb|CD985784.1|CD985784
EST:     ACTGGGATATTCTTCCCCCTAAGCAAATCAAGGACCCAGAGGCTAAGAAG                         CCTGAGGACTGGGATGACAAGGAATACATTCCTGACCCTGAGGACAAGAAG
genomic: ACTGGGATATTCTTCCCCCTAAGCAAATCAAGGACCCAGAGGCTAAGAAGgtgaatacat ... atgattgtagCCTGAGGACTGGGATGACAAGGAATACATTCCTGACCCTGAGGACAAGAAG
EST: gi|58029459|gb|CX724886.1|CX724886
EST:     ACTGGGATATTCTTCCCCCTAAGCAAATCAAGGACCCAGAGGCTAAGAAG                         CCTGAGGACTGGGATGACAAGGAATACATTCCTGACCCTGAGGACAAGAAG
genomic: ACTGGGATATTCTTCCCCCTAAGCAAATCAAGGACCCAGAGGCTAAGAAGgtgaatacat ... atgattgtagCCTGAGGACTGGGATGACAAGGAATACATTCCTGACCCTGAGGACAAGAAG
EST: gi|67010625|gb|CO439374.1|CO439374
EST:     ACTGGGATATTCTTCCCCCTAAGCAAATCAAGGACCCAGAGGCTAAGAAG                         CCTGAGGACTGGGATGACAAGGAATACATTCCTGACCCTGAGGACAAGAAG
genomic: ACTGGGATATTCTTCCCCCTAAGCAAATCAAGGACCCAGAGGCTAAGAAGgtgaatacat ... atgattgtagCCTGAGGACTGGGATGACAAGGAATACATTCCTGACCCTGAGGACAAGAAG
EST: gi|32848163|gb|CD987844.1|CD987844
EST:     ACTGGGATATTCTTCCCCCTAAGAAAATCAAGGACCCAGAGGCTAAGAAG                         CCTGAGGACTGGGATGACAAGGA
genomic: ACTGGGATATTCTTCCCCCTAAGCAAATCAAGGACCCAGAGGCTAAGAAGgtgaatacat ... atgattgtagCCTGAGGACTGGGATGACAAGGA
EST: gi|32945066|gb|CF049885.1|CF049885
EST:     ACTGGGATATTCTTCCCCCTAAGCAAATCAAGGACCCAGAGGCTAAGAAG                         CCTGAGGACTGGGATGACAAGGAATACATTCCTGACCCTGAGGACAAGAAG
genomic: ACTGGGATATTCTTCCCCCTAAGCAAATCAAGGACCCAGAGGCTAAGAAGgtgaatacat ... atgattgtagCCTGAGGACTGGGATGACAAGGAATACATTCCTGACCCTGAGGACAAGAAG
EST: gi|148935865|gb|EC879913.2|EC879913
EST:     ACTGGGATATTCTTCCCCCTAAGCAA-TCAAGGACCCAGAGGCTAAGAAG                         CCTGAGGACTGGGATGACAAGGA-TACATTCCTGACCCTGANGACAAGAAG
genomic: ACTGGGATATTCTTCCCCCTAAGCAAATCAAGGACCCAGAGGCTAAGAAGgtgaatacat ... atgattgtagCCTGAGGACTGGGATGACAAGGAATACATTCCTGACCCTGAGGACAAGAAG
EST: gi|149097674|gb|EE183578.2|EE183578
EST:     ACTGGGATATTCTTCCCCCTAAGCAAATCAAGGACCCAGAGGCTAAGAAG                         CCTGAGGACTGGGATGACAAGGAATACATTCCTG
genomic: ACTGGGATATTCTTCCCCCTAAGCAAATCAAGGACCCAGAGGCTAAGAAGgtgaatacat ... atgattgtagCCTGAGGACTGGGATGACAAGGAATACATTCCTG
EST: gi|149011835|gb|EE042440.2|EE042440
EST:     ACTGGGATATTCTTCCCCCTAAGCAAATCAAGGACCCAGAGGCTAAGAAG                         CCCTGAGGACTGGGATGACAAAGGAA
genomic: ACTGGGATATTCTTCCCCCTAAGCAAATCAAGGACCCAGAGGCTAAGAAGgtgaatacat ... atgattgtagCC-TGAGGACTGGGATGACAA-GGAA
EST: gi|4837470|gb|AI670560.1|AI670560
EST:     ACTGGGATATTCTTCCCCCTAAGCAAATCAAGGACCCAGAGGCTAAGAAG                         CCTGAGGACTGGGATGACAAGGAATACATTCCTGACCCTGAGGACAAGAAG
genomic: ACTGGGATATTCTTCCCCCTAAGCAAATCAAGGACCCAGAGGCTAAGAAGgtgaatacat ... atgattgtagCCTGAGGACTGGGATGACAAGGAATACATTCCTGACCCTGAGGACAAGAAG
EST: gi|149084306|gb|EE173743.2|EE173743
EST:     ACTGGGATATTCTTCCCCCTAAGCAAATCAAGGACCCAGAGGCTAAGAAG                         CCTGANGACTGGGAT
genomic: ACTGGGATATTCTTCCCCCTAAGCAAATCAAGGACCCAGAGGCTAAGAAGgtgaatacat ... atgattgtagCCTGAGGACTGGGAT
EST: gi|148935504|gb|EC879545.2|EC879545
EST:     ACTGGGATATTCTTCCCCCTAAGCAAATCAAGGACCCAGAGGCTAAGAAG                         CCTGAGGACTGGGATGANCA-GGAATACATTCCTGACCCTGA
genomic: ACTGGGATATTCTTCCCCCTAAGCAAATCAAGGACCCAGAGGCTAAGAAGgtgaatacat ... atgattgtagCCTGAGGACTGGGATGA-CAAGGAATACATTCCTGACCCTGA
EST: gi|211311765|gb|FL424550.1|FL424550
EST:     ACTGGGATATTCTTCCCCCTAAGCAAATCAAGGACCCAGAGGCTAAGAAG                         CCTGAGGACTGGGATGACAAGGAATACATTCCTGACCCTGAGGACAAGAAG
genomic: ACTGGGATATTCTTCCCCCTAAGCAAATCAAGGACCCAGAGGCTAAGAAGgtgaatacat ... atgattgtagCCTGAGGACTGGGATGACAAGGAATACATTCCTGACCCTGAGGACAAGAAG
EST: gi|60672264|gb|DN475030.1|DN475030
EST:     ACTGGGATATTCTTCCCCCTAAGCAAATCAAGGACCCAGAGGCTAAGAAG                         CCTGAGGACTGGGATGACAAGGAATACATTCCTGACCCTGAGGACAAGAAG
genomic: ACTGGGATATTCTTCCCCCTAAGCAAATCAAGGACCCAGAGGCTAAGAAGgtgaatacat ... atgattgtagCCTGAGGACTGGGATGACAAGGAATACATTCCTGACCCTGAGGACAAGAAG

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), 49 (downstream exon)
Score: 177

CAGCATTCTCATCGATAATGAAGAGAAGCAAACTGGCAGCATCTATGAGCACTGGGATATTCTTCCCCCTAAGCAAATCAAGGACCCAGAGGCTAAGAAGgtgaatacat ... atgattgtagCCTGAGGACTGGGATGACAAGGAATACATTCCTGACCCTGAGGACAAGAAGCCAGAG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 274

CAGCATTCTCATCGATAATGAAGAGAAGCAAACTGGCAGCATCTATGAGCACTGGGATATTCTTCCCCCTAAGCAAATCAAGGACCCAGAGGCTAAGAAGgtgaatacat ... atgattgtagCCTGAGGACTGGGATGACAAGGAATACATTCCTGACCCTGAGGACAAGAAGCCAGAG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 338

CAGCATTCTCATCGATAATGAAGAGAAGCAAACTGGCAGCATCTATGAGCACTGGGATATTCTTCCCCCTAAGCAAATCAAGGACCCAGAGGCTAAGAAGgtgaatacat ... atgattgtagCCTGAGGACTGGGATGACAAGGAATACATTCCTGACCCTGAGGACAAGAAGCCAGAG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 1852

CAGCATTCTCATCGATAATGAAGAGAAGCAAACTGGCAGCATCTATGAGCACTGGGATATTCTTCCCCCTAAGCAAATCAAGGACCCAGAGGCTAAGAAGgtgaatacat ... atgattgtagCCTGAGGACTGGGATGACAAGGAATACATTCCTGACCCTGAGGACAAGAAGCCAGAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttcttttcttgaacctgtttgtaataattgaggtttatgtgttgatgattgtagCCTGAGGACTGGGATGACAAGGAATACATTCCTGACCCTGAGGACAAGAAGCCAGAG
                                        tgttgat  putative branch site (score: 1852)
                tgtttgtaataatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgaatacataatatttattgttgtgaatttcttttcttgaacctgtttgtaataattgaggtttatgtgttgatgattgtagCCTGAGGACTGGGATGACAAGGAATACATTCCTGACCCTGAGGACAAGAAGCCAGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGC