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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacacaatctacatcttctttttctccagtacatgctggcagcgacatgtatctcgtttgatatggcgatgacgggtctctggacatcagGAGGGTACGGAACAATGGAAGAACTGTTAGAGATGATAACGTGGTCACAGCTCGGAATTCATGACAAACCA

Basic information

species Zea mays
transcript GRMZM2G008726_T01
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G008726_T01 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os01g51210.2 (Oryza sativa), 3'ss of exon 3
-----gtacacaat-ctacatcttctttttctccagt----acatgctggcagcgacatgtatctcgtttgatatggcgatgacgggtctctggacatcagGAGGGTACGGAACAATGGAAGAACTGTTAGAGATGATAACGTGGTCACAGCTCGGAATTCATGACAAACCA
       || || | |||||| || | ||  | |  |    ||  |||   |     |   | |  | || || |   ||  ||   | | ||||||  ||||||||| ||||||||||| ||  |||||||||||||||| |||||||| || ||||||||||||||||||
gtattacactcagttctacatgttttcttgatactatttgaacgggctaatatttcaaaccaccatgcttaat-tactgacaacttttttgtggacaatagGAGGGTATGGAACAATGGAGGAGTTGTTAGAGATGATAACTTGGTCACAACTTGGAATTCATGACAAACCA

upper sequence: GRMZM2G008726_T01 (Zea mays), 3'ss of exon 4
lower sequence: AT5G11950.1 (Arabidopsis thaliana), 3'ss of exon 4
gtacacaatctacatcttctttttctccagtacatgctggcagcgacatgtatctcgtttgatat-ggcgatgacgggtctctggacatcagGAGGGTACGGAACAATGGAAGAACTGTTAGAGATGATAACGTGGTCACAGCTCGGAATTCATGACAAACCA
           | | |   ||       | | |  |||    |  | |  |      |||| |||     |  |||||  | ||    |||||||| || ||||||||||| || ||||| ||||||||||| |||||||| || || || ||| | ||  | 
------gtgagaaaacgctttaaaactgaatcctagctaattgttaaagttgaaagttttggtatcaaaaactacggggttttg---ttcagGAGGTTATGGAACAATGGAGGAGCTGTTGGAGATGATAACATGGTCACAACTTGGTATCCATAAGAAGACG
















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|211040038|gb|FK962663.1|FK962663
EST:     GAGGAAAGCTGAGATGGCACGGCAAGCTGATGCCTTCATAGCTCTTCCTG                         GAGGGTACGGAACAATGGAAGAACTGT
genomic: GAGGAAAGCTGAGATGGCACGGCAAGCTGATGCCTTCATAGCTCTTCCTGgtacacaatc ... tggacatcagGAGGGTACGGAACAATGGAAGAACTGT
EST: gi|211166478|gb|FK962667.1|FK962667
EST:     GAGGAAAGCTGAGATGGCACGGCAAGCTGATGCCTTCATAGCTCTTCCTG                         GAGGGTACGGAACAATGGAAGAACTGTTA
genomic: GAGGAAAGCTGAGATGGCACGGCAAGCTGATGCCTTCATAGCTCTTCCTGgtacacaatc ... tggacatcagGAGGGTACGGAACAATGGAAGAACTGTTA
EST: gi|211166479|gb|FK962668.1|FK962668
EST:     GAGGAAAGCTGAGATGGCACGGCAAGCTGATGCCTTCATAGCTCTTCCTG                         GAGGGTACGGAACAATGG
genomic: GAGGAAAGCTGAGATGGCACGGCAAGCTGATGCCTTCATAGCTCTTCCTGgtacacaatc ... tggacatcagGAGGGTACGGAACAATGG
EST: gi|211166480|gb|FK962669.1|FK962669
EST:     GAGGAAAGCTGAGATGGCACGGCAAGCTGATGCCTTCATAGCTCTTCCTG                         GAGGGTACGGAA
genomic: GAGGAAAGCTGAGATGGCACGGCAAGCTGATGCCTTCATAGCTCTTCCTGgtacacaatc ... tggacatcagGAGGGTACGGAA
EST: gi|211166481|gb|FK962670.1|FK962670
EST:     GAGGAAAGCTGATATGGCACGGCAAGCTGATGCCTTCATAGCTCTTCCTG                         GAGGGTACGGAACAATSGAAGAACTGTTAGAGATGATAACGTGGTCACAGC
genomic: GAGGAAAGCTGAGATGGCACGGCAAGCTGATGCCTTCATAGCTCTTCCTGgtacacaatc ... tggacatcagGAGGGTACGGAACAATGGAAGAACTGTTAGAGATGATAACGTGGTCACAGC
EST: gi|211040039|gb|FK962664.1|FK962664
EST:     GAGGAAAGCTGAGATGGCACGGCAAGCTGATGCCTTCATAGCTCTTCCTG                         GAGGGTACGGAACAATGGAAGAACTGTTAGAG
genomic: GAGGAAAGCTGAGATGGCACGGCAAGCTGATGCCTTCATAGCTCTTCCTGgtacacaatc ... tggacatcagGAGGGTACGGAACAATGGAAGAACTGTTAGAG
EST: gi|211040034|gb|FK962659.1|FK962659
EST:     GAGGAAAGCTGAGATGGCACGGCAAGCTGATGCCTTCATAGCTCTTCCTG                         GAGGGTACGGAACAATG
genomic: GAGGAAAGCTGAGATGGCACGGCAAGCTGATGCCTTCATAGCTCTTCCTGgtacacaatc ... tggacatcagGAGGGTACGGAACAATG
EST: gi|211166482|gb|FK962671.1|FK962671
EST:     GAGGAAAGCTGAGATGGCACGGCAAGCTGATGCCTTCATAGCTCTTCCTG                         GAGGGTACGGAACAATGGAAGAACTGTTAGAGATGATAACGT
genomic: GAGGAAAGCTGAGATGGCACGGCAAGCTGATGCCTTCATAGCTCTTCCTGgtacacaatc ... tggacatcagGAGGGTACGGAACAATGGAAGAACTGTTAGAGATGATAACGT
EST: gi|211040040|gb|FK962665.1|FK962665
EST:     GAGGAAAGCTGAGATGGCACGGCAAGCTGATGCCTTCATAGCTCTTCCTG                         GAGGGTACGGAACAATGGAAGAACTGTT
genomic: GAGGAAAGCTGAGATGGCACGGCAAGCTGATGCCTTCATAGCTCTTCCTGgtacacaatc ... tggacatcagGAGGGTACGGAACAATGGAAGAACTGTT
EST: gi|211040031|gb|FK962656.1|FK962656
EST:     KAGGAAAGCTGAGATGGCACGGCAAGCTGATGCCTTCATAGCTCTTCCTG                         GAGGGTACGGAACAATGGAAGAWCTGTTAGAGTATGATAACGTGGTCACAG
genomic: GAGGAAAGCTGAGATGGCACGGCAAGCTGATGCCTTCATAGCTCTTCCTGgtacacaatc ... tggacatcagGAGGGTACGGAACAATGGAAGAACTGTTAGAG-ATGATAACGTGGTCACAG

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), 48 (downstream exon)
Score: 29

ATATCTGGTGCTAGCGTTGGAGAAGTTAAGGTTGTCTCCGACATGCACGAGAGGAAAGCTGAGATGGCACGGCAAGCTGATGCCTTCATAGCTCTTCCTGgtacacaatc ... tggacatcagGAGGGTACGGAACAATGGAAGAACTGTTAGAGATGATAACGTGGTCACAGCTCGGAATTCATGACAAACCA


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 38

ATATCTGGTGCTAGCGTTGGAGAAGTTAAGGTTGTCTCCGACATGCACGAGAGGAAAGCTGAGATGGCACGGCAAGCTGATGCCTTCATAGCTCTTCCTGgtacacaatc ... tggacatcagGAGGGTACGGAACAATGGAAGAACTGTTAGAGATGATAACGTGGTCACAGCTCGGAATTCATGACAAACCA


Block sizes: 48 (upstream exon), 48 (downstream exon)
Score: 69

ATATCTGGTGCTAGCGTTGGAGAAGTTAAGGTTGTCTCCGACATGCACGAGAGGAAAGCTGAGATGGCACGGCAAGCTGATGCCTTCATAGCTCTTCCTGgtacacaatc ... tggacatcagGAGGGTACGGAACAATGGAAGAACTGTTAGAGATGATAACGTGGTCACAGCTCGGAATTCATGACAAACCA


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 43

ATATCTGGTGCTAGCGTTGGAGAAGTTAAGGTTGTCTCCGACATGCACGAGAGGAAAGCTGAGATGGCACGGCAAGCTGATGCCTTCATAGCTCTTCCTGgtacacaatc ... tggacatcagGAGGGTACGGAACAATGGAAGAACTGTTAGAGATGATAACGTGGTCACAGCTCGGAATTCATGACAAACCA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctggcagcgacatgtatctcgtttgatatggcgatgacgggtctctggacatcagGAGGGTACGGAACAATGGAAGAACTGTTAGAGATGATAACGTGGTCACAGCTCGGAATTCATGACAAACCA
                    gtttgat  putative branch site (score: 43)
                                         tctct  putative PPT
                     tttgatat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtacacaatctacatcttctttttctccagtacatgctggcagcgacatgtatctcgtttgatatggcgatgacgggtctctggacatcagGAGGGTACGGAACAATGGAAGAACTGTTAGAGATGATAACGTGGTCACAGCTCGGAATTCATGACAAACCA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTC