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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttttattaatttgaaattgtactatataatctgatgtgcactctagttacacctatggtcttctgaatctggtatgtaattatcttgtttcattttgcagGTTTCCCTATACTTGGAATAGAATGGCAAAAAATGGAAAATCCTGATCTCCGCAAGGCAATGGGAATGAAAGCTAACCAAAAGGGTGTTCGGATACGAAG

Basic information

species Zea mays
transcript GRMZM2G165969_T01
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G165969_T01 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os06g12780.1 (Oryza sativa), 3'ss of exon 3
--ttttattaatttgaaattgtactatataatctgatgtgcactctagttacacctatggtcttctgaatctggtatgtaattatcttgtttcattttgcagGTTTCCCTATACTTGGAATAGAATGGCAAAAAATGGAAAATCCTGATCTCCGCAAGGCAATGGGAATGAAAGCTAACCAAAAGGGTGTTCGGATACGAAG
    |  ||  |   ||    |  |  || ||    |   ||     | ||  |  ||  ||      || || | ||| |||  |||  ||| |||||||||||| ||||||||||||||||||||||| ||||||||||||||||||||||| |||||||||||||||||| || ||||||||||||||||  |  ||||
aaaatgttttgtggtaatcctttttccattattaacttcacatctatgatattctgattttccatgctatttgct-tgttatttcctttattc-ttttgcagGTTTTCCTATACTTGGAATAGAATGGCAGAAAATGGAAAATCCTGATCTCCGAAAGGCAATGGGAATGAAATCTGACCAAAAGGGTGTTCGTGTCAGAAG

upper sequence: GRMZM2G165969_T01 (Zea mays), 3'ss of exon 4
lower sequence: GLYMA05G01930.1 (Glycine max), 3'ss of exon 3
---ttttattaatttgaaattgtactatataatctgatgtgcactcta-gttacacctatggtcttctgaatctggt---atgtaatta-----tcttgtttcattttgc----agGTTTCCCTATACTTGGAATAGAATGGCAAAAAATGGAAAATCCTGATCTCCGCAAGGCAATGGGAATGAAAGCTAACCAAAAGGGTGTTCGGATACGAAG
    | |  ||  | | || |    | ||  || | |  |  ||   | | ||| |  |   | ||  ||||   ||   ||| | | |     |  | | ||  | |||    ||| |||||||| |||||  | || ||||| |||||||||||||||||||| || | ||| ||||| |||||| || | || || ||||| || ||  ||||
gtaatatggtagctaggaactaagatgta-gatttcacttttacaagatgctac-ctgagcatttttagaattaagttttatgcactcagatctttctttctctatctgctgttagGATTCCCTATTCTTGGGGTTGAGTGGCAGAAAATGGAAAATCCTGATCTGCGAATGGCCATGGGCATGAAACCTGATCAGAAAGGTGTGCGCATTAGAAG

upper sequence: GRMZM2G165969_T01 (Zea mays), 3'ss of exon 4
lower sequence: GLYMA17G09970.1 (Glycine max), 3'ss of exon 3
--------------ttttattaatttg-aaattgtactat-ataatctgatgt-gcactctagttacacctatggtcttctgaatctggtatgtaattatcttgtttcattttgcagGTTTCCCTATACTTGGAATAGAATGGCAAAAAATGGAAAATCCTGATCTCCGCAAGGCAATGGGAATGAAAGCTAACCAAAAGGGTGTTCGGATACGAAG
                  | |||  || | |||  ||| | | ||  || | |   |   |  ||| |  |   || || || | |||  || |   | |||   |    | |  ||| |||||||| |||||  | || |||||||||||||||||||||||||| || | ||||| ||| |||||| || |||| || ||||| || ||  ||||
gtaatatggtagctacaaactaagatgtagatttcacttttacaagatgctatcagagcatttttagaattgaagttttatgca-ctgagatctttctttctcaatctgctgt-tagGATTCCCTATTCTTGGGGTTGAGTGGCAAAAAATGGAAAATCCTGATCTGCGAATGGCAACGGGCATGAAACCTGACCAGAAAGGTGTGCGTATTAGAAG

upper sequence: GRMZM2G165969_T01 (Zea mays), 3'ss of exon 4
lower sequence: PP1S176_87V6.1 (Physcomitrella patens), 3'ss of exon 4
ttttattaatttgaaattgtactatataatctgatgtgcactctagttacacctatggtcttctgaatctggtatgtaattatcttgtttc--attttgcagGTTTCCCTATACTTGGAATAGAATGGCAAAAAATGGAAAATCCTGATCTCCGCAAGGCAATGGGAATGAAAGCTAACCAAAAGGGTGTTCGGATACGAAG
   | | |    ||   ||||   ||   | || ||   |||     |      | | | |            |||   |     || | |  |  ||||||| || || ||  | || || ||||||||||| |||||||| |||||||| || |||||  ||||||||||    | ||| || |||||||| |||||| |
gggtttcatggcgaggctgta--gtagcctgtggtgcttacttcgagtcagtacacgatgtgggtggataatcatgcggtgtatgtgatgcgaacattgcagGGTTTCCGATTTTGGGTATCGAATGGCAAAAGATGGAAAACCCTGATCTTCGGAAGGCGCTGGGAATGAAGAGCACCCAGAAAGGTGTTCGCATACGACG

upper sequence: GRMZM2G165969_T01 (Zea mays), 3'ss of exon 4
lower sequence: PP1S1_203V6.2 (Physcomitrella patens), 3'ss of exon 4
----ttttattaatttgaaattgtacta---tataatctgatgtgcactctagttacacctatggtcttctgaatctggtatgtaattatcttgtttcattttgcagGTTTCCCTATACTTGGAATAGAATGGCAAAAAATGGAAAATCCTGATCTCCGCAAGGCAATGGGAATGAAAGCTAACCAAAAGGGTGTTCGGATACGAAG
       | |||   |||  || ||| |   |    ||     |     || |||  |   || ||   |  | |   |   ||| || |        | | |||||| ||||| ||  | || || ||||||||||| |||||||||||||||||||| |||||  |||||||||| |  | ||| || || ||||| |||||| |
acctgaatgttatagtgaggttctacaagcttgggctccccgatctgggctggttttatg-atagttgccccactacagcgcgtacttgtga------actatgcagGATTCCCCATTTTAGGTATTGAATGGCAAAAGATGGAAAATCCTGATCTCCGGAAGGCGCTGGGAATGAAGGGCATCCAGAAAGGCGTTCGTATACGACG

upper sequence: GRMZM2G165969_T01 (Zea mays), 3'ss of exon 4
lower sequence: PP1S176_111V6.1 (Physcomitrella patens), 3'ss of exon 1
ttttattaatttgaaattgtactatataatctgatgtgcactctagttacacctatggtcttctgaatctggtatgtaattatcttgtttc--attttgcagGTTTCCCTATACTTGGAATAGAATGGCAAAAAATGGAAAATCCTGATCTCCGCAAGGCAATGGGAATGAAAGCTAACCAAAAGGGTGTTCGGATACGAAG
   | | |    ||   ||||   ||   | || ||   |||            | | |||            |||   |     || | |  |  ||||||| || || ||  | || || |||||||||||||||||||| |||||||| || |||||  ||||||||||    | | | || |||||||| |||||| |
gggtttcatggcgaggctgta--gtagcctgtggtgcttacttcgagccagtacacgatctgggtggataatcatgcggtgtatgtgatgcgaacattgcagGGTTTCCGATTTTGGGTATCGAATGGCAAAAAATGGAAAACCCTGATCTTCGGAAGGCGCTGGGAATGAAGAGCACCAAGAATGGTGTTCGCATACGACG

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|31364573|gb|CD448928.1|CD448928
EST:     AGTTATTAACCACTTCATTGAAGATTACAAAAAATCTGGAGAATACACAG                         GTTTCCCTATACTTGGAATAGAATGGCAAAAAATGGAAAATCCTGATCTC
genomic: AGTTATTAACCACTTCATTGAAGATTACAAAAAATCTGGAGAATACACAGgtaccttcct ... cattttgcagGTTTCCCTATACTTGGAATAGAATGGCAAAAAATGGAAAATCCTGATCTC




















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), 47 (downstream exon)
Score: 157

TCTCTTAAACATGAAGATGCAGAGAACATAGGCTATGTTATACCCACCCCAGTTATTAACCACTTCATTGAAGATTACAAAAAATCTGGAGAATACACAGgtaccttcct ... cattttgcagGTTTCCCTATACTTGGAATAGAATGGCAAAAAATGGAAAATCCTGATCTCCGCAAGGCAATGGGAATGAAAGCTAACCAAAAGGGTGTTCGGATACGAAG


Block sizes: 49 (upstream exon), 45 (downstream exon)
Score: 74

TCTCTTAAACATGAAGATGCAGAGAACATAGGCTATGTTATACCCACCCCAGTTATTAACCACTTCATTGAAGATTACAAAAAATCTGGAGAATACACAGgtaccttcct ... cattttgcagGTTTCCCTATACTTGGAATAGAATGGCAAAAAATGGAAAATCCTGATCTCCGCAAGGCAATGGGAATGAAAGCTAACCAAAAGGGTGTTCGGATACGAAG


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 85

TCTCTTAAACATGAAGATGCAGAGAACATAGGCTATGTTATACCCACCCCAGTTATTAACCACTTCATTGAAGATTACAAAAAATCTGGAGAATACACAGgtaccttcct ... cattttgcagGTTTCCCTATACTTGGAATAGAATGGCAAAAAATGGAAAATCCTGATCTCCGCAAGGCAATGGGAATGAAAGCTAACCAAAAGGGTGTTCGGATACGAAG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 86

TCTCTTAAACATGAAGATGCAGAGAACATAGGCTATGTTATACCCACCCCAGTTATTAACCACTTCATTGAAGATTACAAAAAATCTGGAGAATACACAGgtaccttcct ... cattttgcagGTTTCCCTATACTTGGAATAGAATGGCAAAAAATGGAAAATCCTGATCTCCGCAAGGCAATGGGAATGAAAGCTAACCAAAAGGGTGTTCGGATACGAAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gttacacctatggtcttctgaatctggtatgtaattatcttgtttcattttgcagGTTTCCCTATACTTGGAATAGAATGGCAAAAAATGGAAAATCCTGATCTCCGCAAGGCAATGGGAATGAAAGCTAACCAAAAGGGTGTTCGGATACGAAG
                                     tcttgtttcatttt  CT-rich tract
                           tatgtaattatctt  TA-rich tract