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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ctacaaacctatgctattgggctagcgctattaaaaaagacatgttttagatgcactgcccacatatgggtcttggcctcatttgctatattgtttccagGTAGCCAGGAATTTGGGGAAGACTTTGCGTGCTTTCCAACCAACCATTAGAGAGATACAG

Basic information

species Zea mays
transcript GRMZM2G151529_T02
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G151529_T02 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os11g37130.1 (Oryza sativa), 3'ss of exon 2
ctacaaacctatgctattgggctagcgctattaaaaaag-acatgtt-ttagatgcactgcccacatatgggtcttggcctcatttgctatattgtttccagGTAGCCAGGAATTTGGGGAAGACTTTGCGTGCTTTCCAACCAACCATTAGAGAGATACAG
 | |     |||  || || |  |  |  | | |  | | || |  |   |      ||  |   |        | || |||| |||||   |||| | ||||||||||||||||||||||||||||||||||||||||| ||||||||||||||| |||||
gttctgctttattttactgtg--aatgaaaatgagcatgtacttcctgccaacctttctatcattacgaactgttaggtctcacttgcttgcttgtatgcagGTAGCCAGGAATTTGGGGAAGACTTTGCGTGCTTTCCAGCCAACCATTAGAGAGCTACAG
















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|211460557|gb|FL352960.1|FL352960
EST:     CATTGGGAGTAGTCGCCTTGTTGGTGTTCGGCCCCAAGGGTCTAGCAGAG                         GTAGCCAGGAATTTGGGGAAGACTTTGCGTGCTTTCCAACCAACCATTAGA
genomic: CATTGG-AGTAGTCGCCTTGTTGGTGTTCGGCCCCAAGGGTCTAGCAGAGgtaaattagc ... ttgtttccagGTAGCCAGGAATTTGGGGAAGACTTTGCGTGCTTTCCAACCAACCATTAGA
EST: gi|211021363|gb|FL343610.1|FL343610
EST:     TCATTGGAGTAGTCGCCTTGTTGGTGTTCGGCCCCAAGGGTCTAGCAGAG                         GTAGCCAGGAATTTGGGGAAGACTTTGCGTGCTTTCCAACCAACCATTAGA
genomic: TCATTGGAGTAGTCGCCTTGTTGGTGTTCGGCCCCAAGGGTCTAGCAGAGgtaaattagc ... ttgtttccagGTAGCCAGGAATTTGGGGAAGACTTTGCGTGCTTTCCAACCAACCATTAGA
EST: gi|211248880|gb|FL353272.1|FL353272
EST:     TCATTGGAGTAGTCGCCTTGTTGGTGTTCGGCCCCAAGGGTCTAGCAGAG                         GTAGCCAGGAATTTGGGGAAGACTTTGCGTGCTTTCCAACCAACCATTAGA
genomic: TCATTGGAGTAGTCGCCTTGTTGGTGTTCGGCCCCAAGGGTCTAGCAGAGgtaaattagc ... ttgtttccagGTAGCCAGGAATTTGGGGAAGACTTTGCGTGCTTTCCAACCAACCATTAGA
EST: gi|67010971|gb|CO439720.1|CO439720
EST:     TCATTGGAGTAGTCGCCTTGTTGGTGTTCGGCCCCAAGGGTCTAGCAGAG                         GTAGCCAGGAATTTGGGGAAGACTTTGCGTGCTTTCCAACCAACCATTAGA
genomic: TCATTGGAGTAGTCGCCTTGTTGGTGTTCGGCCCCAAGGGTCTAGCAGAGgtaaattagc ... ttgtttccagGTAGCCAGGAATTTGGGGAAGACTTTGCGTGCTTTCCAACCAACCATTAGA
EST: gi|149077405|gb|EE166095.2|EE166095
EST:     TCATTGGAGTAGTCGCCTTGTTGGTGTTCGGCCCCAAGGGTCTAGCAGAG                         GTAGCCAGGAATTTGGGGAAGACTTTGCGTGCTTTCCAACCAACCATTAGA
genomic: TCATTGGAGTAGTCGCCTTGTTGGTGTTCGGCCCCAAGGGTCTAGCAGAGgtaaattagc ... ttgtttccagGTAGCCAGGAATTTGGGGAAGACTTTGCGTGCTTTCCAACCAACCATTAGA
EST: gi|211314764|gb|FL362709.1|FL362709
EST:     TCATTGGAGTAGTCGCCTTGTTGGTGTTCGGCCCCAAGGGTCTAGCAGAG                         GTAGCCAGGAATTTGGGGAAGACTTTGCGTGCTTTCCAACCAACCATTAGA
genomic: TCATTGGAGTAGTCGCCTTGTTGGTGTTCGGCCCCAAGGGTCTAGCAGAGgtaaattagc ... ttgtttccagGTAGCCAGGAATTTGGGGAAGACTTTGCGTGCTTTCCAACCAACCATTAGA
EST: gi|71433878|gb|DR814928.1|DR814928
EST:     TCATTGGAGTAGTCGCCTTGTTGGTGTTCGGCCCCAAGGGTCTAGCAGAG                         GTAGCCAGGAATTTGGGGAAGACTTTGCGTGCTTTCCAACCAACCATTAGA
genomic: TCATTGGAGTAGTCGCCTTGTTGGTGTTCGGCCCCAAGGGTCTAGCAGAGgtaaattagc ... ttgtttccagGTAGCCAGGAATTTGGGGAAGACTTTGCGTGCTTTCCAACCAACCATTAGA
EST: gi|211322619|gb|FL345967.1|FL345967
EST:     TCATTGGAGTAGTCGCCTTGTTGGTGTTCGGCCCCAAGGGTCTAGCAGAG                         GTAGCCAGGAATTTGGGGAAGACTTTGCGTGCTTTCCAACCAACCATTAGA
genomic: TCATTGGAGTAGTCGCCTTGTTGGTGTTCGGCCCCAAGGGTCTAGCAGAGgtaaattagc ... ttgtttccagGTAGCCAGGAATTTGGGGAAGACTTTGCGTGCTTTCCAACCAACCATTAGA
EST: gi|211510099|gb|FL332415.1|FL332415
EST:     TCATTGGAGTAGTCGCCTTGTTGGTGTTCGGCCCCAAGGGTCTAGCAGAG                         GTAGCCAGGAATTTGGGGAAGACTTTGCGTGCTTTCCAACCAACCATTAGA
genomic: TCATTGGAGTAGTCGCCTTGTTGGTGTTCGGCCCCAAGGGTCTAGCAGAGgtaaattagc ... ttgtttccagGTAGCCAGGAATTTGGGGAAGACTTTGCGTGCTTTCCAACCAACCATTAGA
EST: gi|89252968|gb|DY624754.1|DY624754
EST:     TCATTGGAGTAGTCGCCTTGTTGGTGTTCGGCCCCAAGGGTCTAGCAGAG                         GTAGCCAGGAATTTGGGGAAGACTTTGCGTGCTTTCCAACCAACCATTAGA
genomic: TCATTGGAGTAGTCGCCTTGTTGGTGTTCGGCCCCAAGGGTCTAGCAGAGgtaaattagc ... ttgtttccagGTAGCCAGGAATTTGGGGAAGACTTTGCGTGCTTTCCAACCAACCATTAGA
EST: gi|211335139|gb|FL316010.1|FL316010
EST:     TCATTGGAGTAGTCGCCTTGTTGGTGTTCGGCCCCAAGGGTCTAGCAGAG                         GTAGCCAGGAATTTGGGGAAGACTTTGCGTGCTTTCCAACCAACCATTAGA
genomic: TCATTGGAGTAGTCGCCTTGTTGGTGTTCGGCCCCAAGGGTCTAGCAGAGgtaaattagc ... ttgtttccagGTAGCCAGGAATTTGGGGAAGACTTTGCGTGCTTTCCAACCAACCATTAGA
EST: gi|93015586|gb|EB641106.1|EB641106
EST:     TCATTGGAGTAGTCGCCTTGTTGGTGTTCGGCCCCAAGGGTCTAGCAGAG                         GTAGCCAGGAATTTGGGGAAGACTTTGCGTGCTTTCCAACCAACCATTAGA
genomic: TCATTGGAGTAGTCGCCTTGTTGGTGTTCGGCCCCAAGGGTCTAGCAGAGgtaaattagc ... ttgtttccagGTAGCCAGGAATTTGGGGAAGACTTTGCGTGCTTTCCAACCAACCATTAGA
EST: gi|211534496|gb|FL328423.1|FL328423
EST:     TCATTGGAGTAGTCGCCTTGTTGGTGTTCGGCCCCAAGGGTCTAGCAGAG                         GTAGCCAGGAATTTGGGGAAGACTTTGCGTGCTTTCCAACCAACCATTAGA
genomic: TCATTGGAGTAGTCGCCTTGTTGGTGTTCGGCCCCAAGGGTCTAGCAGAGgtaaattagc ... ttgtttccagGTAGCCAGGAATTTGGGGAAGACTTTGCGTGCTTTCCAACCAACCATTAGA
EST: gi|211419512|gb|FL330466.1|FL330466
EST:     TCATTGGAGTAGTCGCCTTGTTGGTGTTCGGCCCCAAGGGTCTAGCAGAG                         GTAGCCAGGAATTTGGGGAAGACTTTGCGTGCTTTCCAACCAACCATTAGA
genomic: TCATTGGAGTAGTCGCCTTGTTGGTGTTCGGCCCCAAGGGTCTAGCAGAGgtaaattagc ... ttgtttccagGTAGCCAGGAATTTGGGGAAGACTTTGCGTGCTTTCCAACCAACCATTAGA
EST: gi|211475488|gb|FL344062.1|FL344062
EST:     TCATTGGAGTAGTCGCCTTGTTGGTGTTCGGCCCCAAGGGTCTAGCAGAG                         GTAGCCAGGAATTTGGGGAAGACTTTGCGTGCTTTCCAACCAACCATTAGA
genomic: TCATTGGAGTAGTCGCCTTGTTGGTGTTCGGCCCCAAGGGTCTAGCAGAGgtaaattagc ... ttgtttccagGTAGCCAGGAATTTGGGGAAGACTTTGCGTGCTTTCCAACCAACCATTAGA
EST: gi|32839855|gb|CD979536.1|CD979536
EST:     TCATTGGAGTAGTCGCCTTGTTGGTGTTCGGCCCCAAGGGTCTAGCAGAG                         GTAGCCAGGAATTTGGGGAAGACTTTGCGTGCTTTCCAACCAACCATTAGA
genomic: TCATTGGAGTAGTCGCCTTGTTGGTGTTCGGCCCCAAGGGTCTAGCAGAGgtaaattagc ... ttgtttccagGTAGCCAGGAATTTGGGGAAGACTTTGCGTGCTTTCCAACCAACCATTAGA
EST: gi|32839856|gb|CD979537.1|CD979537
EST:     TCATTGGAGTAGTCGCCTTGTTGGTGTTCGGCCCCAAGGGTCTAGCAGAG                         GTAGCCAGGAATTTGGGGAAGACTTTGCGTGCTTTCCATCCAACCATTAGA
genomic: TCATTGGAGTAGTCGCCTTGTTGGTGTTCGGCCCCAAGGGTCTAGCAGAGgtaaattagc ... ttgtttccagGTAGCCAGGAATTTGGGGAAGACTTTGCGTGCTTTCCAACCAACCATTAGA
EST: gi|211534335|gb|FL321029.1|FL321029
EST:     CATTGGAGTAGTCGCCTTGTTGGTGTTCGGCCCCAAGGGTCTGAGCAGAG                         GTAGCCAGGAATTTGGGGAAGACTTTGCGTGCTTTCAAACCAACCATTAG
genomic: CATTGGAGTAGTCGCCTTGTTGGTGTTCGGCCCCAAGGGTCT-AGCAGAGgtaaattagc ... ttgtttccagGTAGCCAGGAATTTGGGGAAGACTTTGCGTGCTTTCCAACCAACCATTAG
EST: gi|94474440|gb|EB703398.1|EB703398
EST:     TCATTGGAGTAGTCGCCTTGTTGGTGTTCGGCCCCAAGGGTCTAGCAGAG                         GTAGCCAGGAATTTGGGGAAGACTTTGCGTGCTTTCCAACCACCCATTAGA
genomic: TCATTGGAGTAGTCGCCTTGTTGGTGTTCGGCCCCAAGGGTCTAGCAGAGgtaaattagc ... ttgtttccagGTAGCCAGGAATTTGGGGAAGACTTTGCGTGCTTTCCAACCAACCATTAGA
EST: gi|211216368|gb|FL354220.1|FL354220
EST:     TCATTGGAGTAGTCGCCTTGTTGGTGTTCGGCCCCAAGGGTCTAGCAGAG                         GTAGCCAGGAATTTGGGGAAGACTTTGCGTGCTTTCCAACCAACCATTAGA
genomic: TCATTGGAGTAGTCGCCTTGTTGGTGTTCGGCCCCAAGGGTCTAGCAGAGgtaaattagc ... ttgtttccagGTAGCCAGGAATTTGGGGAAGACTTTGCGTGCTTTCCAACCAACCATTAGA
EST: gi|211132274|gb|FL314469.1|FL314469
EST:     TCATTGGAGTAGTCGCCTTGTTGGTGTTCGGCCCCAAGGGTCTAGCAGAG                         GTAGCCAGGAATTTGGGGAAGACTTTGCGTGCTTTCCAACCAACCATTAGA
genomic: TCATTGGAGTAGTCGCCTTGTTGGTGTTCGGCCCCAAGGGTCTAGCAGAGgtaaattagc ... ttgtttccagGTAGCCAGGAATTTGGGGAAGACTTTGCGTGCTTTCCAACCAACCATTAGA
EST: gi|89252133|gb|DY623919.1|DY623919
EST:     CATTGGAGTAGTCGCCTTGTTGGTGTTCGGGCCCCAAGGGTCTAGCAGAG                         GTAGCCAGGAATTTGGGGAAGACTTTGCGTGCTTTTCCA-CCACCCATTAA
genomic: CATTGGAGTAGTCGCCTTGTTGGTGTTCGG-CCCCAAGGGTCTAGCAGAGgtaaattagc ... ttgtttccagGTAGCCAGGAATTTGGGGAAGACTTTGCGTGCTTT-CCAACCAACCATTAG
EST: gi|211301723|gb|FL323893.1|FL323893
EST:     TCATTGGAGTAGTCGCCTTGTTGGTGTTCGGCCCCAAGGGTCTAGCAGAG                         GTAGCCAGGAATTTGGGGGAAGACTTTGCGTGCTTTCCAACCAACCATTAG
genomic: TCATTGGAGTAGTCGCCTTGTTGGTGTTCGGCCCCAAGGGTCTAGCAGAGgtaaattagc ... ttgtttccagGTAGCCAGGAATTTGGGG-AAGACTTTGCGTGCTTTCCAACCAACCATTAG
EST: gi|21843269|gb|BQ703850.1|BQ703850
EST:     TCATTGGAGTAGTCGCCTTGTTGGTGTTCGGCCCCAAGGGTCTAGCAGAG                         GTAGCCAGGAATTTGGGGAAGACTTTGCGTGCTTTCCAACCAACCATTAGA
genomic: TCATTGGAGTAGTCGCCTTGTTGGTGTTCGGCCCCAAGGGTCTAGCAGAGgtaaattagc ... ttgtttccagGTAGCCAGGAATTTGGGGAAGACTTTGCGTGCTTTCCAACCAACCATTAGA

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: 47 (upstream exon), 49 (downstream exon)
Score: 41

AAACGTTATATGTGCTTCCCTGTTCGGAGTTGGAGCTCCCGAAGCACTGGTCATTGGAGTAGTCGCCTTGTTGGTGTTCGGCCCCAAGGGTCTAGCAGAGgtaaattagc ... ttgtttccagGTAGCCAGGAATTTGGGGAAGACTTTGCGTGCTTTCCAACCAACCATTAGAGAGATACAG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 72

AAACGTTATATGTGCTTCCCTGTTCGGAGTTGGAGCTCCCGAAGCACTGGTCATTGGAGTAGTCGCCTTGTTGGTGTTCGGCCCCAAGGGTCTAGCAGAGgtaaattagc ... ttgtttccagGTAGCCAGGAATTTGGGGAAGACTTTGCGTGCTTTCCAACCAACCATTAGAGAGATACAG


Block sizes: 48 (upstream exon), 43 (downstream exon)
Score: 49

AAACGTTATATGTGCTTCCCTGTTCGGAGTTGGAGCTCCCGAAGCACTGGTCATTGGAGTAGTCGCCTTGTTGGTGTTCGGCCCCAAGGGTCTAGCAGAGgtaaattagc ... ttgtttccagGTAGCCAGGAATTTGGGGAAGACTTTGCGTGCTTTCCAACCAACCATTAGAGAGATACAG


Block sizes: 48 (upstream exon), 48 (downstream exon)
Score: 108

AAACGTTATATGTGCTTCCCTGTTCGGAGTTGGAGCTCCCGAAGCACTGGTCATTGGAGTAGTCGCCTTGTTGGTGTTCGGCCCCAAGGGTCTAGCAGAGgtaaattagc ... ttgtttccagGTAGCCAGGAATTTGGGGAAGACTTTGCGTGCTTTCCAACCAACCATTAGAGAGATACAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttagatgcactgcccacatatgggtcttggcctcatttgctatattgtttccagGTAGCCAGGAATTTGGGGAAGACTTTGCGTGCTTTCCAACCAACCATTAGAGAGATACAG
                                             ttgtttcc  CT-rich tract
                                         tatattgttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ctacaaacctatgctattgggctagcgctattaaaaaagacatgttttagatgcactgcccacatatgggtcttggcctcatttgctatattgtttccagGTAGCCAGGAATTTGGGGAAGACTTTGCGTGCTTTCCAACCAACCATTAGAGAGATACAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA
ctacaaa
- - - - ctatgct
- - - - - - - - - - - - - - - -taaaaaa
- - - - - - - - - - - - - - - - - - - - catgttt
- - - - - - - - - - - - - - - - - - - - - - - - -gatgcac
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ccacata