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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...agattagcaaggtcctaatgaatgttgtagcttgcagttactcctacattgcattatggaatgttttttctgagtgacaagttttttttttttactacagGCTGGAGTTCTGTCTGGTGATGTTAGCGACATTGTACTTCTTGATGTGACCCCCTTGTCCCTAGGTTTGGAGACACTGGGTGGTGTCATGACCAAGATTA

Basic information

species Zea mays
transcript GRMZM2G079668_T01
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G079668_T01 (Zea mays), 3'ss of exon 6
lower sequence: LOC_Os05g23740.1 (Oryza sativa), 3'ss of exon 6
agattagcaaggtcctaatgaatgttgtagcttgcagttactcctacattgcattatggaatgt-tttttctgagtgacaagtttttt----------ttttttactacagGCTGGAGTTCTGTCTGGTGATGTTAGCGACATTGTACTTCTTGATGTGACCCCCTTGTCCCTAGGTTTGGAGACACTGGGTGGTGTCATGACCAAGATTA
||| | || |||| ||| | | | || ||| | | | ||||| | | |||| ||| | | | |||| || |||||| ||||| ||||||||||||| ||||||||||| ||||||||||| || || | || || ||||||||||||||||||||||| |||||||||||||
----------tgtctcactgg-tgttctaggattgattatcttctagagtcagaaagcaaatgtactctactgaactacagaatatctgactggcaaaattttgacaacagGCAGGAGTGTTGTCTGGTGATGTGAGCGACATTGTTCTTCTTGATGTAACACCACTTTCTCTGGGTTTGGAGACACTGGGTGGTGTGATGACCAAGATTA

upper sequence: GRMZM2G079668_T01 (Zea mays), 3'ss of exon 6
lower sequence: PP1S153_153V6.1 (Physcomitrella patens), 3'ss of exon 4
--agattagcaaggtcctaatgaatgttgtagcttgcagttactcctacattgcattatggaatgttttttctgagtgacaagttttttt--tttttactacagGCTGGAGTTCTGTCTGGTGATGTTAGCGACATTGTACTTCTTGATGTGACCCCCTTGTCCCTAGGTTTGGAGACACTGGGTGGTGTCATGACCAAGATTA
| |||||||| | | | || | || | | ||||| || || || || ||| ||| | || | | ||||| || ||| || ||||||| || ||||||||||| || || || ||||| || |||| || ||||||||||| ||||| ||||| ||||| ||||| |
gtggtttagcaagagg-tgtcggggttggtggtgtgtgcgtgcgttgtcattg--ttgcggg-tgggcagcacgaatgagaaggacggggggtgttgaatgcagGCCGGTGTTTTGGCTGGTGAAGTGAGCGACATTGTTCTGCTGGACGTGACGCCTCTGTCTCTGGGTTTGGAGACGCTGGGGGGTGTGATGACGAAGATCA

upper sequence: GRMZM2G079668_T01 (Zea mays), 3'ss of exon 6
lower sequence: PP1S6_146V6.1 (Physcomitrella patens), 3'ss of exon 4
---------------------------------------------------------agattagcaaggt---cctaatgaatgttgtagcttgcagttactcctacattgcatt--atggaatgtt-------ttttctgagtgacaagttttttttttttactacagGCTGGAGTTCTGTCTGGTGATGTTAGCGACATTGTACTTCTTGATGTGACCCCCTTGTCCCTAGGTTTGGAGACACTGGGTGGTGTCATGACCAAGATTA
| |||| | | ||||||| | ||| | || ||| | | | | |||| | | ||||||| | | | || | |||||||||||||| ||| || ||||||| || ||||||||||| ||||| |||||||| || |||| | ||||||||||| |||||||||| ||||| |||||||
gtttgaaattttacctcgatacctactcatctctgtcacgagtatggatggctaaggggtttagtttgttattcctaatggggg--gtatcctgaggttgttttagtagtctgatgaatggcttatcatcgacattttctgtattaacaattgtgggaaattactacagGCTGGTGTTTTGGCTGGTGAAGTCAGCGACATTGTTCTTCTGGATGTGACGCCTCTGTCTTTGGGTTTGGAGACGTTGGGTGGTGTGATGACGAAGATTA

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|13557623|gb|BG548979.1|BG548979
EST:     ATGTGACAGTCAACCCTGATGAGGTTGTTGCACTTGGAGCAGCTGTGCAG                         GCTGGAGTTCTGTCTGGTGATGTTAGCGACATTTTTCTTCTTGATGTGACC
genomic: ATGTGACAGTCAACCCTGATGAGGTTGTTGCACTTGGAGCAGCTGTGCAGgtcagttcac ... tttactacagGCTGGAGTTCTGTCTGGTGATGTTAGCGACATTGTACTTCTTGATGTGACC
EST: gi|31356114|gb|CD440471.1|CD440471
EST:     ATGTGACAGTCAACCCTGATGAGGTTGTTGCACTTGGAGCAGCTGTGCAG                         GCTGGAGTTCTGTCTGGCGATGTTAGCGACATTGTACTTCTTGATGTGACC
genomic: ATGTGACAGTCAACCCTGATGAGGTTGTTGCACTTGGAGCAGCTGTGCAGgtcagttcac ... tttactacagGCTGGAGTTCTGTCTGGTGATGTTAGCGACATTGTACTTCTTGATGTGACC
EST: gi|67039401|gb|CO465656.1|CO465656
EST:     ATGTGACAGTCAACCCTGATGAGGTTGTTGCACTTGGAGCAGCTGTGCAG                         GCTGGAGTTCTGTCTGGTGATGTTAGCGACATTGTACTTCTTGATGTGACC
genomic: ATGTGACAGTCAACCCTGATGAGGTTGTTGCACTTGGAGCAGCTGTGCAGgtcagttcac ... tttactacagGCTGGAGTTCTGTCTGGTGATGTTAGCGACATTGTACTTCTTGATGTGACC
EST: gi|67018243|gb|CO446992.1|CO446992
EST:     ATGTGACAGTCAACCCTGATGAGGTTGTTGCACTTGGAGCAGCTGTGCAG                         GCTGGAGTTCTGTCTGGTGATGTTAGCGACATTGTACTTCTTGATGTGACC
genomic: ATGTGACAGTCAACCCTGATGAGGTTGTTGCACTTGGAGCAGCTGTGCAGgtcagttcac ... tttactacagGCTGGAGTTCTGTCTGGTGATGTTAGCGACATTGTACTTCTTGATGTGACC
EST: gi|78080017|gb|DV508429.1|DV508429
EST:     ATGTGACAGTCAACCCTGATGAGGTTGTTGCACTTGGAGCAGCTGTGCAG                         GCTGGAGTTCTGTCTGGTGATGTTAGCGACATTGTACTTCTTGATGTGACC
genomic: ATGTGACAGTCAACCCTGATGAGGTTGTTGCACTTGGAGCAGCTGTGCAGgtcagttcac ... tttactacagGCTGGAGTTCTGTCTGGTGATGTTAGCGACATTGTACTTCTTGATGTGACC

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), 45 (downstream exon)
Score: 59

AATACCAGCTGTTCAGGAGCTTGTCAAGAAAATGACAGGAAAGGACCCCAATGTGACAGTCAACCCTGATGAGGTTGTTGCACTTGGAGCAGCTGTGCAGgtcagttcac ... tttactacagGCTGGAGTTCTGTCTGGTGATGTTAGCGACATTGTACTTCTTGATGTGACCCCCTTGTCCCTAGGTTTGGAGACACTGGGTGGTGTCATGACCAAGATTA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 324

AATACCAGCTGTTCAGGAGCTTGTCAAGAAAATGACAGGAAAGGACCCCAATGTGACAGTCAACCCTGATGAGGTTGTTGCACTTGGAGCAGCTGTGCAGgtcagttcac ... tttactacagGCTGGAGTTCTGTCTGGTGATGTTAGCGACATTGTACTTCTTGATGTGACCCCCTTGTCCCTAGGTTTGGAGACACTGGGTGGTGTCATGACCAAGATTA


Block sizes: 49 (upstream exon), 46 (downstream exon)
Score: 38

AATACCAGCTGTTCAGGAGCTTGTCAAGAAAATGACAGGAAAGGACCCCAATGTGACAGTCAACCCTGATGAGGTTGTTGCACTTGGAGCAGCTGTGCAGgtcagttcac ... tttactacagGCTGGAGTTCTGTCTGGTGATGTTAGCGACATTGTACTTCTTGATGTGACCCCCTTGTCCCTAGGTTTGGAGACACTGGGTGGTGTCATGACCAAGATTA


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 233

AATACCAGCTGTTCAGGAGCTTGTCAAGAAAATGACAGGAAAGGACCCCAATGTGACAGTCAACCCTGATGAGGTTGTTGCACTTGGAGCAGCTGTGCAGgtcagttcac ... tttactacagGCTGGAGTTCTGTCTGGTGATGTTAGCGACATTGTACTTCTTGATGTGACCCCCTTGTCCCTAGGTTTGGAGACACTGGGTGGTGTCATGACCAAGATTA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

acattgcattatggaatgttttttctgagtgacaagttttttttttttactacagGCTGGAGTTCTGTCTGGTGATGTTAGCGACATTGTACTTCTTGATGTGACCCCCTTGTCCCTAGGTTTGGAGACACTGGGTGGTGTCATGACCAAGATTA
                                    ttttttttttttacta  CT-rich tract
 acaagttttttttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
agattagcaaggtcctaatgaatgttgtagcttgcagttactcctacattgcattatggaatgttttttctgagtgacaagttttttttttttactacagGCTGGAGTTCTGTCTGGTGATGTTAGCGACATTGTACTTCTTGATGTGACCCCCTTGTCCCTAGGTTTGGAGACACTGGGTGGTGTCATGACCAAGATTA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA