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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tccgtcgtcccgccatcatcactgagtttgctgtattggtcagaggtgcaaactaactccatcgatgccgcggattaatgaaccggccgtctttctgcagGTTACCTGAACGACCCCGAGTCGACGAAGAACACCATCGACAAGGACGGCTGGCTGCACACCGGAGACATCGGCTACGTGGACGACGACGACGAGATCTT

Basic information

species Zea mays
transcript GRMZM2G075333_T01
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G075333_T01 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os02g08100.1 (Oryza sativa), 3'ss of exon 3
tccgtcgtcccg----ccatcatcactgagtttgctgtattggtcagaggtgcaaactaactccatcgatgccgcggattaatgaaccggccgtctttctgcagGTTACCTGAACGACCCCGAGTCGACGAAGAACACCATCGACAAGGACGGCTGGCTGCACACCGGAGACATCGGCTACGTGGACGACGACGACGAGATCTT
 | |  || | |       ||| ||||||   ||   | |   |||||      |   ||    ||   || | || | | | || | |   |   || |||||| || ||||| || || ||| |||| ||||||||||||||| ||||||| ||||||||||||||||||||||||| ||| ||||||||||||||||||||
-ctgcagtacagaattttgtcaccactgaaactgtcttctccttcagaaacagcaggaaatg--attcttggc-cgtactgacgagctgtggggaattttgcagGCTATCTGAATGATCCTGAGGCGACCAAGAACACCATCGACGAGGACGGGTGGCTGCACACCGGAGACATCGGCTTCGTCGACGACGACGACGAGATCTT

upper sequence: GRMZM2G075333_T01 (Zea mays), 3'ss of exon 3
lower sequence: PP1S167_96V6.1 (Physcomitrella patens), 3'ss of exon 3
-------------------------------------------------------tccgtcgtcccgccatcatcactgagtttgct---gtattggtcaga---ggtgcaaactaactccatcg--atgccgcggattaatgaaccggccgtctttctgcagGTTACCTGAACGACCCCGAGTCGACGAAGAACACCATCGACAAGGACGGCTGGCTGCACACCGGAGACATCGGCTACGTGGACGACGACGACGAGATCTT
                                                       |   | || |  ||||   ||     |||| |   ||||||     |   | |||   | |   | |  |  | ||    ||  || ||   |   |   || |||||||||| ||||  | || ||  | ||    |||||||||||||||||||| |  ||||||||||||||| ||| || | | || || ||||| ||||| ||
gttcgttaccgtcgtcctcaacgggtcgattgtttgcagcaaagtatgtttgacatttatggttct-ccatatccatatgatttgtttgagtattgtgtgcacttgatgctgtcaattacaagtgggaggctcaagagaaacga--tgcttggtcttgtgcagGTTACTTGAATAATCCTGAAGCAACAGCCAACACCATCGACAAGGACGGTTTTCTGCACACCGGAGACGTCGCCTTCATTGATGAGGACGAGGAGATGTT
















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|91872376|gb|EB402333.1|EB402333
EST:     CCGGAACCAGCCCGGCGAGATCTGCATCCGCGGGGAGCAGATCATGAAAG                         GTTACCTGAACGACCCCGAGTCGACGAAGAACACCATCGACAAGGACGGCT
genomic: CCGGAACCAGCCCGGCGAGATCTGCATCCGCGGGGAGCAGATCATGAAAGgtgcgccgca ... ctttctgcagGTTACCTGAACGACCCCGAGTCGACGAAGAACACCATCGACAAGGACGGCT
EST: gi|91053777|gb|EB164195.1|EB164195
EST:     GATCATGAAAG                         GTTACCTGAACGACCCCGAGTCGACGAAGAACACCATCGACAAGGACGGCT
genomic: GATCATGAAAGgtgcgccgca ... ctttctgcagGTTACCTGAACGACCCCGAGTCGACGAAGAACACCATCGACAAGGACGGCT
EST: gi|149109199|gb|EE293185.2|EE293185
EST:     CCGCGGGGAGCAGATCATGAAAG                         GTTACCTGAACGACCCCGAGTCGACGAAGAACACCATCGACAAGGACGGCT
genomic: CCGCGGGGAGCAGATCATGAAAGgtgcgccgca ... ctttctgcagGTTACCTGAACGACCCCGAGTCGACGAAGAACACCATCGACAAGGACGGCT
EST: gi|71450117|gb|DR831167.1|DR831167
EST:     CCGGAACCAGCCCGGCGAGATCTGCATCCGCGGGGAGCAGATCATGAAAG                         GTTACCTGAACGACCCCGAGTCGACGAAGAACACCATCGACAAGGACGGCT
genomic: CCGGAACCAGCCCGGCGAGATCTGCATCCGCGGGGAGCAGATCATGAAAGgtgcgccgca ... ctttctgcagGTTACCTGAACGACCCCGAGTCGACGAAGAACACCATCGACAAGGACGGCT
EST: gi|94474315|gb|EB703273.1|EB703273
EST:     CCGGAACCAGCCCGGCGAGATCTGCATCCGCGGGGAGCAGATCATGAAAG                         GTTACCTGAACGACCCCGAGTCGACGAAGAACACCATCGACAAGGACGGCT
genomic: CCGGAACCAGCCCGGCGAGATCTGCATCCGCGGGGAGCAGATCATGAAAGgtgcgccgca ... ctttctgcagGTTACCTGAACGACCCCGAGTCGACGAAGAACACCATCGACAAGGACGGCT
EST: gi|71774578|gb|DR972456.1|DR972456
EST:     CCGCGGGGAGCAGATCATGAAAG                         GTTACCTGAACGACCCCGAGTCGACGAAGAACACCATCGACAAGGACGGCT
genomic: CCGCGGGGAGCAGATCATGAAAGgtgcgccgca ... ctttctgcagGTTACCTGAACGACCCCGAGTCGACGAAGAACACCATCGACAAGGACGGCT
EST: gi|76287908|gb|DV027476.1|DV027476
EST:     ACCAGCCCGGCGAGATCTGCATCCGCGGGGAGCAGATCATGAAAG                         GTTACCTGAACGACCCCGAGTCGACGAAGAACACCATCGACAAGGACGGCT
genomic: ACCAGCCCGGCGAGATCTGCATCCGCGGGGAGCAGATCATGAAAGgtgcgccgca ... ctttctgcagGTTACCTGAACGACCCCGAGTCGACGAAGAACACCATCGACAAGGACGGCT
EST: gi|78109184|gb|DV527601.1|DV527601
EST:     CCGGAACCAGCCCGGCGAGATCTGCATCCGCGGGGAGCAGATCATGAAAG                         GTTACCTGAACGACCCCGAGTCGACGAAGAACACCATCGACAAGGACGGCT
genomic: CCGGAACCAGCCCGGCGAGATCTGCATCCGCGGGGAGCAGATCATGAAAGgtgcgccgca ... ctttctgcagGTTACCTGAACGACCCCGAGTCGACGAAGAACACCATCGACAAGGACGGCT
EST: gi|18660517|gb|BM500903.1|BM500903
EST:     CCGGAACCAGCCCGGCGAGATCTGCATCCGCGGGGAGCAGATCATGAAAG                         GTTACCTGAACGACCCCGAGTCGACGAAGAACACCATCGACAAGGACGGCT
genomic: CCGGAACCAGCCCGGCGAGATCTGCATCCGCGGGGAGCAGATCATGAAAGgtgcgccgca ... ctttctgcagGTTACCTGAACGACCCCGAGTCGACGAAGAACACCATCGACAAGGACGGCT

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: 44 (upstream exon), 38 (downstream exon)
Score: 9

CGGAACGCGGAGCTGAAGATCGTCGACCCCGACACCGGCGCCGCCCTCGGCCGGAACCAGCCCGGCGAGATCTGCATCCGCGGGGAGCAGATCATGAAAGgtgcgccgca ... ctttctgcagGTTACCTGAACGACCCCGAGTCGACGAAGAACACCATCGACAAGGACGGCTGGCTGCACACCGGAGACATCGGCTACGTGGACGACGACGACGAGATCTT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 263

CGGAACGCGGAGCTGAAGATCGTCGACCCCGACACCGGCGCCGCCCTCGGCCGGAACCAGCCCGGCGAGATCTGCATCCGCGGGGAGCAGATCATGAAAGgtgcgccgca ... ctttctgcagGTTACCTGAACGACCCCGAGTCGACGAAGAACACCATCGACAAGGACGGCTGGCTGCACACCGGAGACATCGGCTACGTGGACGACGACGACGAGATCTT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 384

CGGAACGCGGAGCTGAAGATCGTCGACCCCGACACCGGCGCCGCCCTCGGCCGGAACCAGCCCGGCGAGATCTGCATCCGCGGGGAGCAGATCATGAAAGgtgcgccgca ... ctttctgcagGTTACCTGAACGACCCCGAGTCGACGAAGAACACCATCGACAAGGACGGCTGGCTGCACACCGGAGACATCGGCTACGTGGACGACGACGACGAGATCTT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 281

CGGAACGCGGAGCTGAAGATCGTCGACCCCGACACCGGCGCCGCCCTCGGCCGGAACCAGCCCGGCGAGATCTGCATCCGCGGGGAGCAGATCATGAAAGgtgcgccgca ... ctttctgcagGTTACCTGAACGACCCCGAGTCGACGAAGAACACCATCGACAAGGACGGCTGGCTGCACACCGGAGACATCGGCTACGTGGACGACGACGACGAGATCTT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtgcaaactaactccatcgatgccgcggattaatgaaccggccgtctttctgcagGTTACCTGAACGACCCCGAGTCGACGAAGAACACCATCGACAAGGACGGCTGGCTGCACACCGGAGACATCGGCTACGTGGACGACGACGACGAGATCTT
                                         ccgtctttct  CT-rich tract
                            attaatgaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tccgtcgtcccgccatcatcactgagtttgctgtattggtcagaggtgcaaactaactccatcgatgccgcggattaatgaaccggccgtctttctgcagGTTACCTGAACGACCCCGAGTCGACGAAGAACACCATCGACAAGGACGGCTGGCTGCACACCGGAGACATCGGCTACGTGGACGACGACGACGAGATCTT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATC
- - - - - -gccatca
- - - - - - - - - - - - - tttgctg
- - - - - - - - - - - - - - - - - - - - - -aggtgca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gatgccg