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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

tCAAGTCACTGGCGCTGTTGGTTGGAGAAGAGAGGGACTTGTGTACAAGAAGAATGAG

Basic information

species Zea mays
transcript GRMZM2G331032_T02
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G331032_T02 (Zea mays), 3'ss of exon 5
lower sequence: LOC_Os02g46510.1 (Oryza sativa), 3'ss of exon 4
----------------------------------------------------------------------------------------------------------------------------------------------------------tCAAGTCACTGGCGCTGTTGGTTGGAGAAGAGAGGGACTTGTGTACAAGAAGAATGAG
                                                                                                                                                           ||||| ||||| ||||||||||||||||||||||| ||| ||||||||||||| |||
gtgagaaaaatgtgacattgaaataagataaccggataaaaagtcacatcaaatagtttgttgctcatttattttgtgtgaaagcatctgaatcattttttttttgttctctgcactgatagCCTTCAGATAAGCCTGTTCCGAATGCCACTCTACAAGTTACTGGTGCTGTTGGTTGGAGAAGAGAGGGTCTTATGTACAAGAAGAACGAG

upper sequence: GRMZM2G331032_T02 (Zea mays), 3'ss of exon 5
lower sequence: AT5G46630.1 (Arabidopsis thaliana), 3'ss of exon 4
-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------tCAAGTCACTGGCGCTGTTGGTTGGAGAAGAGAGGGACTTGTGTACAAGAAGAATGAG
                                                                                                                                                                                          ||||| || || ||||||||||||||||||||||| ||||  ||||| |||||||||
gtaaaggcatctatttgtttgtgtatacaacagattttgtaattgtgttggtgtgtggttcttcgaagttaagcagtatttcccgcaataaatagagattatgttgcttcttcactagatatgtttgcattcataagcttcttttcattacagCCAAAAGACAAACCTGTTCCAAATGCAACATTACAAGTTACAGGTGCTGTTGGTTGGAGAAGAGAGGGCCTTGCTTACAAAAAGAATGAG

upper sequence: GRMZM2G331032_T02 (Zea mays), 3'ss of exon 5
lower sequence: Vv02s0012g00910.t01 (Vitis vinifera), 3'ss of exon 4
----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------tCAAGTCACTGGCGCTGTTGGTTGGAGAAGAGAGGGACTTGTGTACAAGAAGAATGAG
                                                                                                                                                                                                                                         ||||| || || |||||||||||||| |||||||| ||||| || || |||||||||
gttagatgtttattttagctatacattttggaatctagtaatttgagcagatgaggcattaccgtggatttctaagttgtacttaatggtttatattttaagtatacattattaaaatgaagattcctttatattaaagtgaattttttattgaagattccttaatactatttttctttaatgtgccaaaatataaatagCCTTCAGATAAACCAGTCCCCAATGCAACTTTACAAGTTACAGGTGCTGTTGGTTGGAGGAGAGAGGGCCTTGTTTATAAAAAGAATGAG

upper sequence: GRMZM2G331032_T02 (Zea mays), 3'ss of exon 5
lower sequence: EFJ22278 (Selaginella moellendorffii), 3'ss of exon 4
---------------------------------------------------------------------------------------tCAAGTCACTGGCGCTGTTGGTTGGAGAAGAGAGGGACTTGTGTACAAGAAGAATGAG
                                                                                        |||||||| || || || || |||||||||||||| ||||| |||||||| ||||||
gtagcgatgtgttgcattgcctggctggttaacagaatttatctctttccagCCCATAGATACAAGACCCCCAGCAAATGCTACTCTCCAAGTCACCGGTGCAGTGGGATGGAGAAGAGAGGGTCTTGTTTACAAGAAAAATGAG

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|71445146|gb|DR826196.1|DR826196
EST:     CCCTCAGAGAAGCCTGTTCCAAATGCGACTCTT                         CAAGTCACTGGCGCTGTTGGTTGGAGAAGAGAGGGACTTGTGTACAAGAAG
genomic: CCCTCAGAGAAGCCTGTTCCAAATGCGACTCTTt ... tCAAGTCACTGGCGCTGTTGGTTGGAGAAGAGAGGGACTTGTGTACAAGAAGAATGAGgtgcttaaac .
EST: gi|149078564|gb|EE167348.2|EE167348
EST:     CCCTCAGAGAAGCCTGTTCCAAATGCGACTCTT                         CAAGTCACTGGCGCTGTTGGTTGGAGAAGAGAGGGACTTGTGTACAAAAAG
genomic: CCCTCAGAGAAGCCTGTTCCAAATGCGACTCTTt ... tCAAGTCACTGGCGCTGTTGGTTGGAGAAGAGAGGGACTTGTGTACAAGAAGAATGAGGTT
EST: gi|149090427|gb|EE179737.2|EE179737
EST:     CCCTCAGAGAAGCCTGTTCCAAATGCGACTCTT                         CAAGTCACTGGCGCTGTTGGTTGGAGAAGAGAGGGACTTGTGTACAAGAAG
genomic: CCCTCAGAGAAGCCTGTTCCAAATGCGACTCTTt ... tCAAGTCACTGGCGCTGTTGGTTGGAGAAGAGAGGGACTTGTGTACAAGAAGAATGAGgtgcttaaac .
EST: gi|76937034|gb|DV175018.1|DV175018
EST:     CCCTCAGAGAAGCCTGTTCCAAATGCGACTCTT                         CAAGTCACTGGCGCTGTTGGTTGGAGAAGAGAGGGACTTGTGTACAAGAAG
genomic: CCCTCAGAGAAGCCTGTTCCAAATGCGACTCTTt ... tCAAGTCACTGGCGCTGTTGGTTGGAGAAGAGAGGGACTTGTGTACAAGAAGAATGAGgtgcttaaac .
EST: gi|71304030|gb|DR788136.1|DR788136
EST:     CCCTCAGAGAAGCCTGTTCCAAATGCGACTCTT                         CAAGTCACTGGCGCTGTTGGTTGGAGAAGAGAGGGACTTGTGTACAAGAAG
genomic: CCCTCAGAGAAGCCTGTTCCAAATGCGACTCTTt ... tCAAGTCACTGGCGCTGTTGGTTGGAGAAGAGAGGGACTTGTGTACAAGAAGAATGAGgtgcttaaac .
EST: gi|91054998|gb|EB165416.1|EB165416
EST:     CCCTCAGAGAAGCCTGTTCCAAATGCGACTCTT                         CAAGTCACTGGCGCTGTTGGTTGGAGAAGAGAGGGACTTGTGTACAAGAAG
genomic: CCCTCAGAGAAGCCTGTTCCAAATGCGACTCTTt ... tCAAGTCACTGGCGCTGTTGGTTGGAGAAGAGAGGGACTTGTGTACAAGAAGAATGAGgtgcttaaac .
EST: gi|149083894|gb|EE173269.2|EE173269
EST:     CCCTCAGAGAAGCCTGTTCCAAATGCGACTCTT                         CAAGTCACTGGCGCTGTTGGTTGGAGAAGAGAGGGACTTGTGTACAAGAAG
genomic: CCCTCAGAGAAGCCTGTTCCAAATGCGACTCTTt ... tCAAGTCACTGGCGCTGTTGGTTGGAGAAGAGAGGGACTTGTGTACAAGAAGAATGAGgtgcttaaac .
EST: gi|76282279|gb|DV021847.1|DV021847
EST:     CCCTCAGAGAAGCCTGTTCCAAATGCGACTCTT                         CAAGTCACTGGCGCTGTTGGTTGGAGAAGAGAGGGACTTGTGTACAAGAAG
genomic: CCCTCAGAGAAGCCTGTTCCAAATGCGACTCTTt ... tCAAGTCACTGGCGCTGTTGGTTGGAGAAGAGAGGGACTTGTGTACAAGAAGAATGAGgtgcttaaac .
EST: gi|211055145|gb|FL320202.1|FL320202
EST:     CCCTCAGAGAAGCCTGTTCCAAATGCGACTCTT                         CAAGTCACTGGCGCTGTTGGTTGGAGAAGAGAGGGACTTGTGTACAAGAAG
genomic: CCCTCAGAGAAGCCTGTTCCAAATGCGACTCTTt ... tCAAGTCACTGGCGCTGTTGGTTGGAGAAGAGAGGGACTTGTGTACAAGAAGAATGAGgtgcttaaac .
EST: gi|14202339|gb|BG836016.1|BG836016
EST:     CCSTCAGAGAAGCCTGTYC-AAATGCGACTCTT                         CAAGTCACTGGCGCTGTTGGTTGGAGAR-AGAGGGACTTGTGTACAA-AAG
genomic: CCCTCAGAGAAGCCTGTTCCAAATGCGACTCTTt ... tCAAGTCACTGGCGCTGTTGGTTGGAGAAGAGAGGGACTTGTGTACAAGAAGAATGAGGTTT
EST: gi|5525788|gb|AI861681.1|AI861681
EST:     CCCTCAGAGAAGCCTGTTCCAAATGCGACTCTT                         CAAGTCACTGGCGCTGTTGGTTGGAGAAGAGAGGGACTTGTGTACAAGAAG
genomic: CCCTCAGAGAAGCCTGTTCCAAATGCGACTCTTt ... tCAAGTCACTGGCGCTGTTGGTTGGAGAAGAGAGGGACTTGTGTACAAGAAGAATGAGgtgcttaaac .
EST: gi|31354959|gb|CD439316.1|CD439316
EST:     CCCTCAGAGAAGCCTGTTCCATATGCGACTCTT                         CAAGTCACTGGCGCTGTTGGTTGGAGAAGAGAGGGACTTGTGTACAAGAAG
genomic: CCCTCAGAGAAGCCTGTTCCAAATGCGACTCTTt ... tCAAGTCACTGGCGCTGTTGGTTGGAGAAGAGAGGGACTTGTGTACAAGAAGAATGAGgtgcttaaac .
EST: gi|76918953|gb|DV167527.1|DV167527
EST:     CCCTCAGAGAAGCCTGTTCCAAATGCGACTCTT                         CAAGTCACTGGCGCTGTTGGTTGGAGAAGAGAGGGACTTGTGTACAAGAAG
genomic: CCCTCAGAGAAGCCTGTTCCAAATGCGACTCTTt ... tCAAGTCACTGGCGCTGTTGGTTGGAGAAGAGAGGGACTTGTGTACAAGAAGAATGAGgtgcttaaac .

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: 33 (upstream exon), 49 (downstream exon)
Score: 365

CCCTCAGAGAAGCCTGTTCCAAATGCGACTCTTt ... tCAAGTCACTGGCGCTGTTGGTTGGAGAAGAGAGGGACTTGTGTACAAGAAGAATGAG


Block sizes: 33 (upstream exon), 48 (downstream exon)
Score: 489

CCCTCAGAGAAGCCTGTTCCAAATGCGACTCTTt ... tCAAGTCACTGGCGCTGTTGGTTGGAGAAGAGAGGGACTTGTGTACAAGAAGAATGAG


Block sizes: 33 (upstream exon), 49 (downstream exon)
Score: 514

CCCTCAGAGAAGCCTGTTCCAAATGCGACTCTTt ... tCAAGTCACTGGCGCTGTTGGTTGGAGAAGAGAGGGACTTGTGTACAAGAAGAATGAG


Block sizes: 33 (upstream exon), 48 (downstream exon)
Score: 433

CCCTCAGAGAAGCCTGTTCCAAATGCGACTCTTt ... tCAAGTCACTGGCGCTGTTGGTTGGAGAAGAGAGGGACTTGTGTACAAGAAGAATGAG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tCAAGTCACTGGCGCTGTTGGTTGGAGAAGAGAGGGACTTGTGTACAAGAAGAATGAG

- - - - - -  GCTGTT
- - - - - - - - - -  TTGGAG
- - - - - - - - - - - TGGAGA
- - - - - - - - - - -  GGAGAA
- - - - - - - - - - - - -  AAGAGA
- - - - - - - - - - - - - -  GAGAGG
- - - - - - - - - - - - - - - - - - - - - - - AAGAAG