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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaacatactgttctcttttggttttaccctgtcaatttcaatgaacctcttaaataagttttcttaatatcatgcttgttcagATAATTGGTATCATTGGGCCTATGGTTATCATAACAGTGATATACTTTAAGAAGAGAAATGTATATGATCTGCATCATGCCATACTAG

Basic information

species Zea mays
transcript GRMZM2G077187_T01
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G077187_T01 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os01g49820.1 (Oryza sativa), 3'ss of exon 2
gtaacatactgttctcttttggttttaccctgtcaatttcaatgaacctct-----taaataagttttcttaata--tcatgcttgttcagATAATTGGTATCATTGGGCCTATGGTTATCATAACAGTGATATACTTTAAGAAGAGAAATGTATATGATCTGCATCATGCCATACTAG
|||| | |   | | ||| | ||| || ||     |||||  |   ||| |     ||| |||  |||||| | |  ||||||||    ||||||||||||||||||| || ||| ||||||| || |  |||||||| |||||||| ||||| |||||| | ||||||||||||||||
gtaa-acatcttacccttctagttctatccaacagatttcctttggcctgtacaggtaattaaagtttcttgaaaattcatgctttcgtagATAATTGGTATCATTGGACCAATGATTATCATCACTGGAATATACTTCAAGAAGAGGAATGTGTATGATTTCCATCATGCCATACTAG
















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|76286378|gb|DV025946.1|DV025946
EST:     ACCTCAGATACCCCATGAAGGGCAATACAGTGCCATTTTGGGCTGTGCCG                         ATAATTGGTATCATTGGGCCTATGGTTATCATAACAGTGATATACTTTAAG
genomic: ACCTCAGATACCCCATGAAGGGCAATACAGTGCCATTTTGGGCTGTGCCGgtaacatact ... gcttgttcagATAATTGGTATCATTGGGCCTATGGTTATCATAACAGTGATATACTTTAAG
EST: gi|14243380|gb|BG841070.2|BG841070
EST:     ACCTCAGATACCCCATGAAGGGCAATACAGTGCCATTTTGGGCTGTGCCG                         ATAATTGGTATCATTGGGCCTATGGTTATCATAACAGTGATATACTTTAAG
genomic: ACCTCAGATACCCCATGAAGGGCAATACAGTGCCATTTTGGGCTGTGCCGgtaacatact ... gcttgttcagATAATTGGTATCATTGGGCCTATGGTTATCATAACAGTGATATACTTTAAG
EST: gi|76935224|gb|DV174245.1|DV174245
EST:     ACCTCAGATACCCCATGAAGGGCAATACAGTGCCATTTTGGGCTGTGCCG                         ATAATTGGTATCATTGGGCCTATGGTTATCATAACA
genomic: ACCTCAGATACCCCATGAAGGGCAATACAGTGCCATTTTGGGCTGTGCCGgtaacatact ... gcttgttcagATAATTGGTATCATTGGGCCTATGGTTATCATAACA
EST: gi|61119018|gb|DN559979.1|DN559979
EST:     ACCTCAGATACCCCATGAAGGGCAACACAGTGCCATTTTGGGCTGTGCCG                         ATAATTGGTATCATTGGGCCTATGGTTATCATAACAGTGATATACTTTAAG
genomic: ACCTCAGATACCCCATGAAGGGCAATACAGTGCCATTTTGGGCTGTGCCGgtaacatact ... gcttgttcagATAATTGGTATCATTGGGCCTATGGTTATCATAACAGTGATATACTTTAAG
EST: gi|78079032|gb|DV507444.1|DV507444
EST:     ACCTCAGATACCCCATGAAGGGCAATACAGTGCCATTTTGGGCTGTGCCG                         ATAATTGGTATCATTGGGCCTATGGTTATCATAACAGTGATATACTTTAAG
genomic: ACCTCAGATACCCCATGAAGGGCAATACAGTGCCATTTTGGGCTGTGCCGgtaacatact ... gcttgttcagATAATTGGTATCATTGGGCCTATGGTTATCATAACAGTGATATACTTTAAG
EST: gi|86467943|gb|DY234313.1|DY234313
EST:     ACCTCAGATACCCCATGAAGGGCAATACAGTGCCATTTTGGGCTGTGCCG                         ATAATTGGTATCATTGGGCCTATGGTTATCATAACAGTGATATACTTTAAG
genomic: ACCTCAGATACCCCATGAAGGGCAATACAGTGCCATTTTGGGCTGTGCCGgtaacatact ... gcttgttcagATAATTGGTATCATTGGGCCTATGGTTATCATAACAGTGATATACTTTAAG
EST: gi|76289091|gb|DV028659.1|DV028659
EST:     ACCTCAGATACCCCATGAAGGGCAATACAGTGCCATTTTGGGCTGTGCCG                         ATAATTGGTATCATTGGGCCTATGGTTATCATAACAGTGATATACTTTAAG
genomic: ACCTCAGATACCCCATGAAGGGCAATACAGTGCCATTTTGGGCTGTGCCGgtaacatact ... gcttgttcagATAATTGGTATCATTGGGCCTATGGTTATCATAACAGTGATATACTTTAAG
EST: gi|24934529|gb|CA452747.1|CA452747
EST:     ACCTCACTTACCCCATGAAGGGCAATACAGTGCCATTTTGGGCTGTGCCG                         ATAATTGGTATCATTGGGCCTATGGTTATCATAACAGTGATATACTTTAAG
genomic: ACCTCAGATACCCCATGAAGGGCAATACAGTGCCATTTTGGGCTGTGCCGgtaacatact ... gcttgttcagATAATTGGTATCATTGGGCCTATGGTTATCATAACAGTGATATACTTTAAG

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), 25 (downstream exon)
Score: 9

TAATATAATAGAACCCTTCCATCGCTTCGTCGGATCAGAAATGATGACAGACCTCAGATACCCCATGAAGGGCAATACAGTGCCATTTTGGGCTGTGCCGgtaacatact ... gcttgttcagATAATTGGTATCATTGGGCCTATGGTTATCATAACAGTGATATACTTTAAGAAGAGAAATGTATATGATCTGCATCATGCCATACTAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 299

TAATATAATAGAACCCTTCCATCGCTTCGTCGGATCAGAAATGATGACAGACCTCAGATACCCCATGAAGGGCAATACAGTGCCATTTTGGGCTGTGCCGgtaacatact ... gcttgttcagATAATTGGTATCATTGGGCCTATGGTTATCATAACAGTGATATACTTTAAGAAGAGAAATGTATATGATCTGCATCATGCCATACTAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 341

TAATATAATAGAACCCTTCCATCGCTTCGTCGGATCAGAAATGATGACAGACCTCAGATACCCCATGAAGGGCAATACAGTGCCATTTTGGGCTGTGCCGgtaacatact ... gcttgttcagATAATTGGTATCATTGGGCCTATGGTTATCATAACAGTGATATACTTTAAGAAGAGAAATGTATATGATCTGCATCATGCCATACTAG


Block sizes: 48 (upstream exon), 47 (downstream exon)
Score: 14

TAATATAATAGAACCCTTCCATCGCTTCGTCGGATCAGAAATGATGACAGACCTCAGATACCCCATGAAGGGCAATACAGTGCCATTTTGGGCTGTGCCGgtaacatact ... gcttgttcagATAATTGGTATCATTGGGCCTATGGTTATCATAACAGTGATATACTTTAAGAAGAGAAATGTATATGATCTGCATCATGCCATACTAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctgtcaatttcaatgaacctcttaaataagttttcttaatatcatgcttgttcagATAATTGGTATCATTGGGCCTATGGTTATCATAACAGTGATATACTTTAAGAAGAGAAATGTATATGATCTGCATCATGCCATACTAG
                                 tcttaat  putative branch site (score: 14)
                                              cttgttc  putative PPT
                     ttaaataagttttctt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaacatactgttctcttttggttttaccctgtcaatttcaatgaacctcttaaataagttttcttaatatcatgcttgttcagATAATTGGTATCATTGGGCCTATGGTTATCATAACAGTGATATACTTTAAGAAGAGAAATGTATATGATCTGCATCATGCCATACTAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGA