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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tttagttgtagttacttcactgtgaccaaatatgtcctattgcctgtgctatgaattcatctgtatggatctcaccgttccctttttgttgtaccatcagGAAAGGATCCAAGAGTGGGGCATCAGGAACATGCCATGGTTGTCGTGGTGCTGGAATGAGAACAATCACAAGACAGATAGGCCTTGGCATGATCCAACAG

Basic information

species Zea mays
transcript GRMZM2G118731_T01
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G118731_T01 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os02g43930.3 (Oryza sativa), 3'ss of exon 4
tttagttgtagttacttcactgtgaccaaatatgtcctattgcctgtgctatg-aattcatctgtatggatctcaccgttccctt--tttgttgtaccatcagGAAAGGATCCAAGAGTGGGGCATCAGGAACATGCCATGGTTGTCGTGGTGCTGGAATGAGAACAATCACAAGACAGATAGGCCTTGGCATGATCCAACAG
  || |||||||  ||  | ||| ||  | | |     |||   | |  | |  | ||    | ||| | |||||| ||| ||||   || ||||||| |||| ||||||||||||||||||||| ||| ||| ||||||||||||| |||||| |||||||||||||| |||||||| || || ||||||||||||||||||
--tacttgtagt-gctcaattgttactcagtttaatgcattcttttttttttctagttttgttatattggtctcactgttgccttacgtttttgtaccttcagTAAAGGATCCAAGAGTGGGGCAGCAGCAACTTGCCATGGTTGTCATGGTGCAGGAATGAGAACAATAACAAGACAAATTGGGCTTGGCATGATCCAACAG
















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|76293182|gb|DV032750.1|DV032750
EST:     ACCAAGAAACTATCTTTATCGCGGAGTGCTTTGTGCTCCAAGTGCAAGGG                         GAAAGGATCCAAGAGTGGGGCATCAGGAACATGCCATGGTTGTCGTGGTGC
genomic: ACCAAGAAACTATCTTTATCGCGGAGTGCTTTGTGCTCCAAGTGCAAGGGgtaagttttt ... gtaccatcagGAAAGGATCCAAGAGTGGGGCATCAGGAACATGCCATGGTTGTCGTGGTGC
EST: gi|18964087|gb|BM660802.1|BM660802
EST:     ACCAAGAAACTATCTTTATCGCGGAGTGCTTTGTGCTCCAAGTGCAAGGG                         GAAAGGATCCAAGAGTGGGGCATCAGGAACATGCCATGGTTGTCGTGGTGC
genomic: ACCAAGAAACTATCTTTATCGCGGAGTGCTTTGTGCTCCAAGTGCAAGGGgtaagttttt ... gtaccatcagGAAAGGATCCAAGAGTGGGGCATCAGGAACATGCCATGGTTGTCGTGGTGC
EST: gi|18963673|gb|BM660567.1|BM660567
EST:     ACCAAGAAACTATCTTTATCGCGGAGTGCTTTGTGCTCCAAGTGCAAGGG                         GAAAGGATCCAAGAGTGGGGCATCAGGAACATGCCATGGTTGTCGTGGTGC
genomic: ACCAAGAAACTATCTTTATCGCGGAGTGCTTTGTGCTCCAAGTGCAAGGGgtaagttttt ... gtaccatcagGAAAGGATCCAAGAGTGGGGCATCAGGAACATGCCATGGTTGTCGTGGTGC
EST: gi|148964320|gb|EC905716.2|EC905716
EST:     ACCAAGAAACTATCTTTATCGCGGAGTGCTTTGTGCTCCAAGTGCAAGGG                         GAAAGGATCCAAGAGTGGGGCATCAGGAACATGCCATGGTTGTCGTGGTGC
genomic: ACCAAGAAACTATCTTTATCGCGGAGTGCTTTGTGCTCCAAGTGCAAGGGgtaagttttt ... gtaccatcagGAAAGGATCCAAGAGTGGGGCATCAGGAACATGCCATGGTTGTCGTGGTGC
EST: gi|31348685|gb|CD433042.1|CD433042
EST:     ACCAAGAAACTATCTTTATCGCGGAGTGCTTTGTGCTCCAAGTGCAAGGG                         GAAAGGATCCAAGAGTGGGGCATCAGGAACATGCCATGGTTGTCGTGGTGC
genomic: ACCAAGAAACTATCTTTATCGCGGAGTGCTTTGTGCTCCAAGTGCAAGGGgtaagttttt ... gtaccatcagGAAAGGATCCAAGAGTGGGGCATCAGGAACATGCCATGGTTGTCGTGGTGC
EST: gi|32930958|gb|CF035770.1|CF035770
EST:     ACCAAGAAACTATCTTTATCGCGGAGTGCTTTGTGCTCCAAGTGCAAGGG                         GAAAGGATCCAAGAGTGGGGCATCAGGAACATGCCATGGTTGTCGTGGTGC
genomic: ACCAAGAAACTATCTTTATCGCGGAGTGCTTTGTGCTCCAAGTGCAAGGGgtaagttttt ... gtaccatcagGAAAGGATCCAAGAGTGGGGCATCAGGAACATGCCATGGTTGTCGTGGTGC
EST: gi|148931484|gb|EC874496.2|EC874496
EST:     ACCAAGAAACTATCTTTATCGCGGAGTGCTTTGTGCTCCAAGTGCAAGGG                         GAAAGGATCCAAGAGTGGGGCATCAGGAACATGCCATGGTTGTCGTGGTGC
genomic: ACCAAGAAACTATCTTTATCGCGGAGTGCTTTGTGCTCCAAGTGCAAGGGgtaagttttt ... gtaccatcagGAAAGGATCCAAGAGTGGGGCATCAGGAACATGCCATGGTTGTCGTGGTGC
EST: gi|149037356|gb|EE155375.2|EE155375
EST:     ACCAAGAAACTATCTTTATCGCGGAGTGCTTTGTGCTCCAAGTGCAAGGG                         GAAAGGATCCAAGAGTGGGGCATCAGGAACATGCCATGGTTGTCGTGGTGC
genomic: ACCAAGAAACTATCTTTATCGCGGAGTGCTTTGTGCTCCAAGTGCAAGGGgtaagttttt ... gtaccatcagGAAAGGATCCAAGAGTGGGGCATCAGGAACATGCCATGGTTGTCGTGGTGC
EST: gi|148955629|gb|EC901294.2|EC901294
EST:     ACCAAGAAACTATCTTTATCGCGGAGTGCTTTGTGCTCCAAGTGCAAGGG                         GAAAGGATCCAAGAGTGGGGCATCAGGAACATGCCATGGTTGTCGTGGTGC
genomic: ACCAAGAAACTATCTTTATCGCGGAGTGCTTTGTGCTCCAAGTGCAAGGGgtaagttttt ... gtaccatcagGAAAGGATCCAAGAGTGGGGCATCAGGAACATGCCATGGTTGTCGTGGTGC
EST: gi|13150523|gb|BG320845.1|BG320845
EST:     ACCAAGAAACTATCTTTATCGCGGAGTGCTTTGTGCTCCAAGTGCAAGGG                         GAAAGGATCCAAGAGTGGGGCATCAGGAACATGCCATGGTTGTCGTGGTGC
genomic: ACCAAGAAACTATCTTTATCGCGGAGTGCTTTGTGCTCCAAGTGCAAGGGgtaagttttt ... gtaccatcagGAAAGGATCCAAGAGTGGGGCATCAGGAACATGCCATGGTTGTCGTGGTGC

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), 49 (downstream exon)
Score: 442

ATGTGGTGCATACTATGAAGGTTTCCTTAGACGATCTGTACAATGGGACAACCAAGAAACTATCTTTATCGCGGAGTGCTTTGTGCTCCAAGTGCAAGGGgtaagttttt ... gtaccatcagGAAAGGATCCAAGAGTGGGGCATCAGGAACATGCCATGGTTGTCGTGGTGCTGGAATGAGAACAATCACAAGACAGATAGGCCTTGGCATGATCCAACAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 564

ATGTGGTGCATACTATGAAGGTTTCCTTAGACGATCTGTACAATGGGACAACCAAGAAACTATCTTTATCGCGGAGTGCTTTGTGCTCCAAGTGCAAGGGgtaagttttt ... gtaccatcagGAAAGGATCCAAGAGTGGGGCATCAGGAACATGCCATGGTTGTCGTGGTGCTGGAATGAGAACAATCACAAGACAGATAGGCCTTGGCATGATCCAACAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 535

ATGTGGTGCATACTATGAAGGTTTCCTTAGACGATCTGTACAATGGGACAACCAAGAAACTATCTTTATCGCGGAGTGCTTTGTGCTCCAAGTGCAAGGGgtaagttttt ... gtaccatcagGAAAGGATCCAAGAGTGGGGCATCAGGAACATGCCATGGTTGTCGTGGTGCTGGAATGAGAACAATCACAAGACAGATAGGCCTTGGCATGATCCAACAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 611

ATGTGGTGCATACTATGAAGGTTTCCTTAGACGATCTGTACAATGGGACAACCAAGAAACTATCTTTATCGCGGAGTGCTTTGTGCTCCAAGTGCAAGGGgtaagttttt ... gtaccatcagGAAAGGATCCAAGAGTGGGGCATCAGGAACATGCCATGGTTGTCGTGGTGCTGGAATGAGAACAATCACAAGACAGATAGGCCTTGGCATGATCCAACAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtgctatgaattcatctgtatggatctcaccgttccctttttgttgtaccatcagGAAAGGATCCAAGAGTGGGGCATCAGGAACATGCCATGGTTGTCGTGGTGCTGGAATGAGAACAATCACAAGACAGATAGGCCTTGGCATGATCCAACAG
                       atctcac  putative branch site (score: 611)
                                ttccctttttgttgt  putative PPT
                                     tttttgtt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tttagttgtagttacttcactgtgaccaaatatgtcctattgcctgtgctatgaattcatctgtatggatctcaccgttccctttttgttgtaccatcagGAAAGGATCCAAGAGTGGGGCATCAGGAACATGCCATGGTTGTCGTGGTGCTGGAATGAGAACAATCACAAGACAGATAGGCCTTGGCATGATCCAACAG

- - - - - - - -ttcactg
- - - - - - - - - - - -gaccaaa
- - - - - - - - - - - - - - - - - - - - tgcctgt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ctgtatg