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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaaccacttcagttcgagtgaatcagtaacttgcttatcctcaatcaattcctgcatgaatgcttatgttgggggactttagGTCGGCCCTCTCCGGTGCTGGCCTGGTGGCTTGTGCCTCTCAAGATCCATCGGGGACATGGATGTTGGAGAGTTCATTGTGCCCATTCCACATGTCAAGC

Basic information

species Zea mays
transcript GRMZM5G836628_T02
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G836628_T02 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os07g49040.1 (Oryza sativa), 3'ss of exon 3
-----------------------------------------------------------------gtaaaccacttcagt-tcgagtgaatcagtaacttgcttatcctcaatcaattcctgcatgaatgct-tatgttgggggactttagGTCGGCCCTCTCCGGTGCTGGCCTGGTGGCTTGTGCCTCTCAAGATCCATCGGGGACATGGATGTTGGAGAGTTCATTGTGCCCATTCCACATGTCAAGC
                                                                 |  |  || | |  | |  ||          | | |   ||  ||  |    |  |||||   || | | || ||      | ||||| || ||||||||||||||||| |||||| ||||||| |||||||| ||||||||||||||||| || |||||||||||||| ||||||||||| ||||
gtaccaattcgccccgcagtttggtagatgatggccagattgaaaaaaagagaggcttcgcttttgcgatgcattgctatgtgaagctttgtttccagtcggccatgttctgttttgtgatgcattgttgttgtttgatgctttgttctagGTTGGTCCTCTCCGGTGCTGGCCAGGTGGCCTGTGCCTTTCAAGATCTATCGGGGACATGGATGTCGGGGAGTTCATTGTGCCGATTCCACATGTGAAGC

upper sequence: GRMZM5G836628_T02 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA20G38270.1 (Glycine max), 3'ss of exon 4
gtaaaccacttcagttcgagtgaatcagtaacttgcttatcctcaatcaattcctgcatgaatgcttatg-----ttgggggactt-tagGTCGGCCCTCTCCGGTGCTGGCCTGGTGGCTTGTGCCTCTCAAGATCCATCGGGGACATGGATGTTGGAGAGTTCATTGTGCCCATTCCACATGTCAAGC
             ||  |    ||||  ||  || |||       |  | ||  |   |      || ||     ||     | || ||||| || ||||| || |||||||||||||| |||||||| || ||||| || || |||| ||| || ||||| || |||||||| || |||||||| ||||
-------------gtatggtgtaatctttatattcctttctaatcaggactttttaactagcctgttttggttccttaatacatttatagGTAGGGCCTCTTCGCTGCTGGCCTGGTGGATTGTGCCTTTCTAGATCAATTGGTGACACGGACGTGGGAGAATTTATTGTGCCAATACCACATGTTAAGC

upper sequence: GRMZM5G836628_T02 (Zea mays), 3'ss of exon 3
lower sequence: Vv14s0060g01580.t01 (Vitis vinifera), 3'ss of exon 4
------------------gtaaaccacttcagttcgagtgaatcagtaacttgcttatcctcaatca-attcctgcatgaatgcttatgttgggggactttagGTCGGCCCTCTCCGGTGCTGGCCTGGTGGCTTGTGCCTCTCAAGATCCATCGGGGACATGGATGTTGGAGAGTTCATTGTGCCCATTCCACATGTCAAGC
                    | || |||  |    ||  |||    ||| |   |  |||    ||      || ||||  | |  ||||    ||  | ||||| ||||| ||||| |||||||||||||| || || ||||| || || || || ||||  ||||| ||||| |||||||| || || |||||||| ||||
gtataacatatttgatgcccatacaactcaaagctgaaagaaattttaattgattattcccttgtcttgaatcttcatgggt-caaatgtatatggtttgtagGTTGGCCCACTCCGCTGCTGGCCTGGTGGATTATGTCTCTCCAGGTCAATTGGTGACACAGATGTGGGAGAATTCATTGTCCCAATACCACATGTTAAGC

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|76018331|gb|DT945501.1|DT945501
EST:     CGGCCAGCGGTGGGGAAGTAGGCCGGCTCAATCTCTTTGGCGGCCAGGAG                         GTCGGCCCTCTCCGGTGCTGGCCTGGTGGCTTGTGCCTCTCAAGATCCATC
genomic: CGGCCAGCGGTGGGGAAGTAGGCCGGCTCAATCTCTTTGGCGGCCAGGAGgtaaaccact ... gggactttagGTCGGCCCTCTCCGGTGCTGGCCTGGTGGCTTGTGCCTCTCAAGATCCATC
EST: gi|93012388|gb|EB637908.1|EB637908
EST:     CGGCCAGCGGTGGGGAAGTAGGCCGGCTCAATCTCTTTGGCGGCCAGGAG                         GTCGGCCCTCTCCGGTGCTGGCCTGGTGGCTTGTGCCTCTCAAGATCCATC
genomic: CGGCCAGCGGTGGGGAAGTAGGCCGGCTCAATCTCTTTGGCGGCCAGGAGgtaaaccact ... gggactttagGTCGGCCCTCTCCGGTGCTGGCCTGGTGGCTTGTGCCTCTCAAGATCCATC
EST: gi|148943613|gb|EC888676.2|EC888676
EST:     CGGCCAGCGGTGGGGAAGTAGGCCGGCTCAATCTCTTTGGCGGCCAGGAG                         GTCGGCCCTCTCCGGTGCTGGCCTGGTGGCTTGTGCCTCTCAAGATCCATC
genomic: CGGCCAGCGGTGGGGAAGTAGGCCGGCTCAATCTCTTTGGCGGCCAGGAGgtaaaccact ... gggactttagGTCGGCCCTCTCCGGTGCTGGCCTGGTGGCTTGTGCCTCTCAAGATCCATC
EST: gi|148932058|gb|EC875401.2|EC875401
EST:     CGGCCAGCGGTGGGGAAGTAGGCCGGCTCAATCTCTTTGGCGGCCAGGAG                         GTCGGCCCTCTCCGGTGCTGGCCTGGTGGCTTGTGCCTCTCAAGATCCATC
genomic: CGGCCAGCGGTGGGGAAGTAGGCCGGCTCAATCTCTTTGGCGGCCAGGAGgtaaaccact ... gggactttagGTCGGCCCTCTCCGGTGCTGGCCTGGTGGCTTGTGCCTCTCAAGATCCATC
EST: gi|71430183|gb|DR811233.1|DR811233
EST:     CGGCCAGCGGTGGGGAAGTAGGCCGGCTCAATCTCTTTGGCGGCCAGGAG                         GTCGGCCCTCTCCGGTGCTGGCCTGGTGGCTTGTGCCTCTCAAGATCCATC
genomic: CGGCCAGCGGTGGGGAAGTAGGCCGGCTCAATCTCTTTGGCGGCCAGGAGgtaaaccact ... gggactttagGTCGGCCCTCTCCGGTGCTGGCCTGGTGGCTTGTGCCTCTCAAGATCCATC
EST: gi|149109561|gb|EE190266.2|EE190266
EST:     CGGCCAGCGGTGGGGAAGTAGGCCGGCTCAATCTCTTTGGCGGCCAGGAG                         GTCGGCCCTCTCCGGTGCTGGCCTGGTGGCTTGTGCCTCTCAAGATCCATC
genomic: CGGCCAGCGGTGGGGAAGTAGGCCGGCTCAATCTCTTTGGCGGCCAGGAGgtaaaccact ... gggactttagGTCGGCCCTCTCCGGTGCTGGCCTGGTGGCTTGTGCCTCTCAAGATCCATC
EST: gi|148967746|gb|EE019020.2|EE019020
EST:     CGGCCAGCGGTGGGGAAGTAGGCCGGCTCAATCTCTTTGGCGGCCAGGAG                         GTCGGCCCTCTCCGGTGCTGGCCTGGTGGCTTGTGCCTCTCAAGATCCCTC
genomic: CGGCCAGCGGTGGGGAAGTAGGCCGGCTCAATCTCTTTGGCGGCCAGGAGgtaaaccact ... gggactttagGTCGGCCCTCTCCGGTGCTGGCCTGGTGGCTTGTGCCTCTCAAGATCCATC
EST: gi|91050128|gb|EB160546.1|EB160546
EST:     CGGCCAGCGGTGGGGAAGTAGGCCGGCTCAATCTCTTTGGCGGCCAGGAG                         GTCGGCCCTCTCCGGTGCTGGCCTGGTGGCTTGTGCCTCTNCA-GATCCAT
genomic: CGGCCAGCGGTGGGGAAGTAGGCCGGCTCAATCTCTTTGGCGGCCAGGAGgtaaaccact ... gggactttagGTCGGCCCTCTCCGGTGCTGGCCTGGTGGCTTGTGCCTCT-CAAGATCCAT
EST: gi|148958254|gb|EC904468.2|EC904468
EST:     CGGCCAGCGGTGGGGAAGTAGGCCGGCTCAATCTCTTTGGCGGCCAGGAG                         GTCGGCCCTCTCCGGTGCTGGCCTGGTGGCTTGTGCCTCTCAAGATCCATC
genomic: CGGCCAGCGGTGGGGAAGTAGGCCGGCTCAATCTCTTTGGCGGCCAGGAGgtaaaccact ... gggactttagGTCGGCCCTCTCCGGTGCTGGCCTGGTGGCTTGTGCCTCTCAAGATCCATC
EST: gi|149014901|gb|EE044621.2|EE044621
EST:     CGGCCAGCGGTGGGGAAGTAGGCCGGCTCAATCTCTTTGGCGGCCAGGAG                         GTCGGCCCTCTCCGGTGCTGGCCTGGTGGCTTGTGCCTCTCAAGATCCATC
genomic: CGGCCAGCGGTGGGGAAGTAGGCCGGCTCAATCTCTTTGGCGGCCAGGAGgtaaaccact ... gggactttagGTCGGCCCTCTCCGGTGCTGGCCTGGTGGCTTGTGCCTCTCAAGATCCATC
EST: gi|78110646|gb|DV529051.1|DV529051
EST:     CGGCCAGCGGTGGGGAAGTAGGCCGGCTCAATCTCTTTGGCGGCCAGGAG                         GTCGGCCCTCTCCGGTGCTGGCCTGGTGGCTTGTGCCTCTCAAGATCCATC
genomic: CGGCCAGCGGTGGGGAAGTAGGCCGGCTCAATCTCTTTGGCGGCCAGGAGgtaaaccact ... gggactttagGTCGGCCCTCTCCGGTGCTGGCCTGGTGGCTTGTGCCTCTCAAGATCCATC
EST: gi|149101969|gb|EE287481.2|EE287481
EST:     CGGCCAGCGGTGGGGAAGTAGGCCGGCTCAATCTCTTTGGCGGCCAGGAG                         GTCGGCCCTCTCCGGTGCTGGCCTGGTGGCTTGTGCCTCTCAAGATCCATC
genomic: CGGCCAGCGGTGGGGAAGTAGGCCGGCTCAATCTCTTTGGCGGCCAGGAGgtaaaccact ... gggactttagGTCGGCCCTCTCCGGTGCTGGCCTGGTGGCTTGTGCCTCTCAAGATCCATC

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: 46 (upstream exon), 49 (downstream exon)
Score: 75

AACCGTGGACCACCGCCTGGAGGAGAATGCAGAGGAGCGGGAGCGCGTCACGGCCAGCGGTGGGGAAGTAGGCCGGCTCAATCTCTTTGGCGGCCAGGAGgtaaaccact ... gggactttagGTCGGCCCTCTCCGGTGCTGGCCTGGTGGCTTGTGCCTCTCAAGATCCATCGGGGACATGGATGTTGGAGAGTTCATTGTGCCCATTCCACATGTCAAGC


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 74

AACCGTGGACCACCGCCTGGAGGAGAATGCAGAGGAGCGGGAGCGCGTCACGGCCAGCGGTGGGGAAGTAGGCCGGCTCAATCTCTTTGGCGGCCAGGAGgtaaaccact ... gggactttagGTCGGCCCTCTCCGGTGCTGGCCTGGTGGCTTGTGCCTCTCAAGATCCATCGGGGACATGGATGTTGGAGAGTTCATTGTGCCCATTCCACATGTCAAGC


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 64

AACCGTGGACCACCGCCTGGAGGAGAATGCAGAGGAGCGGGAGCGCGTCACGGCCAGCGGTGGGGAAGTAGGCCGGCTCAATCTCTTTGGCGGCCAGGAGgtaaaccact ... gggactttagGTCGGCCCTCTCCGGTGCTGGCCTGGTGGCTTGTGCCTCTCAAGATCCATCGGGGACATGGATGTTGGAGAGTTCATTGTGCCCATTCCACATGTCAAGC


Block sizes: 47 (upstream exon), 47 (downstream exon)
Score: 52

AACCGTGGACCACCGCCTGGAGGAGAATGCAGAGGAGCGGGAGCGCGTCACGGCCAGCGGTGGGGAAGTAGGCCGGCTCAATCTCTTTGGCGGCCAGGAGgtaaaccact ... gggactttagGTCGGCCCTCTCCGGTGCTGGCCTGGTGGCTTGTGCCTCTCAAGATCCATCGGGGACATGGATGTTGGAGAGTTCATTGTGCCCATTCCACATGTCAAGC




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aacttgcttatcctcaatcaattcctgcatgaatgcttatgttgggggactttagGTCGGCCCTCTCCGGTGCTGGCCTGGTGGCTTGTGCCTCTCAAGATCCATCGGGGACATGGATGTTGGAGAGTTCATTGTGCCCATTCCACATGTCAAGC
 cagtaac  putative branch site (score: 52)
               aatcaatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaaaccacttcagttcgagtgaatcagtaacttgcttatcctcaatcaattcctgcatgaatgcttatgttgggggactttagGTCGGCCCTCTCCGGTGCTGGCCTGGTGGCTTGTGCCTCTCAAGATCCATCGGGGACATGGATGTTGGAGAGTTCATTGTGCCCATTCCACATGTCAAGC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGA