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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gaattttctgcttgtttgatctaccattgctgtcagcgtgcatattatagaaaaatatgcacattgtcttattccttaatgtatctttgtgcaagtgtagGTAATTCTGGATTCCTTCCAGCACTGTTGCCTGACCAGGTCCGAAAGCTAAAGCAGCTCAGCGTGCTAACTCTGGCAGAGTCAACTAAG

Basic information

species Zea mays
transcript GRMZM2G171745_T02
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G171745_T05 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os07g30840.4 (Oryza sativa), 3'ss of exon 2
gaattttctgcttgtttgatctaccattgctgtcagcgtgcatattatagaaaaatatgcacattgtcttattccttaat-gtatc---tttgtgcaagtgtagGTAATTCTGGATTCCTTCCAGCACTGTTGCCTGACCAGGTCCGAAAGCTAAAGCAGCTCAGCGTGCTAACTCTGGCAGAGTCAACTAAG
   | | | | ||||   ||   |  ||  |   |   | || || |  | | || ||| |||||  ||  ||| ||||| || |    |||    |  |||||||||||||||    || || ||| |||| ||||| || ||||| ||||| ||||| ||||||||||||||| |||| |||||||| |||
---tctgcagtttgtggtattctctgtttatagtaatat-cagataagtgcagaacatgaacatttactgtttcattaattgtttttaattttcatacatgtagGTAATTCTGGCAATCTCCCTGCATTGTTACCTGATCAAGTCCGGAAGCTGAAGCAACTCAGCGTGCTAACTTTGGCTGAGTCAACCAAG
















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|13178371|gb|BG349629.1|BG349629
EST:     ACTGGACTTGCTCCGGCTCTTCGCCTACGGTACCCTGAATGACTACAAGA                         GTAATTCTGGATTCCTTCCAGCACTGTTGCCTGACCAGGTCCGAAAGCTAA
genomic: ACTGGACTTGCTCCGGCTCTTCGCCTACGGTACCCTGAATGACTACAAGAgtaagattgt ... gcaagtgtagGTAATTCTGGATTCCTTCCAGCACTGTTGCCTGACCAGGTCCGAAAGCTAA
EST: gi|211178527|gb|FK980685.1|FK980685
EST:     ACTGGACTTGCTCCGGCTCTTCGCCTACGGTACCCTGAATGACTACAAGA                         GTAATTCTGGATTCCTTCCAGCACTGTTGCCTGACCAGGTCCGAAAGCTAA
genomic: ACTGGACTTGCTCCGGCTCTTCGCCTACGGTACCCTGAATGACTACAAGAgtaagattgt ... gcaagtgtagGTAATTCTGGATTCCTTCCAGCACTGTTGCCTGACCAGGTCCGAAAGCTAA
EST: gi|78118434|gb|DV536820.1|DV536820
EST:     ACTGGACTTGCTCCGGCTCTTCGCCTACGGTACCCTGAATGACTACAAGA                         GTAATTCTGGATTCCTTCCAGCACTGTTGCCTGACCAGGTCCGAAAGCTAA
genomic: ACTGGACTTGCTCCGGCTCTTCGCCTACGGTACCCTGAATGACTACAAGAgtaagattgt ... gcaagtgtagGTAATTCTGGATTCCTTCCAGCACTGTTGCCTGACCAGGTCCGAAAGCTAA
EST: gi|211178524|gb|FK980682.1|FK980682
EST:     ACTGGACTTGCTCCGGCTCTTCGCCTACGGTACCCTGAATGACTACAAGA                         GTAATTCTGGATTCCTTCCAGCACTGTTGCCTGACCAGGTCCGAAAGCTAA
genomic: ACTGGACTTGCTCCGGCTCTTCGCCTACGGTACCCTGAATGACTACAAGAgtaagattgt ... gcaagtgtagGTAATTCTGGATTCCTTCCAGCACTGTTGCCTGACCAGGTCCGAAAGCTAA
EST: gi|211180924|gb|FK980686.1|FK980686
EST:     ACTGGACTTGCTCCGGCTCTTCGCCTACGGTACCCTGAATGACTACAAGA                         GTAATTCTGGATTCCTTCCAGCACTGTTGCCTGACCAGGTCCGAAAGCTAA
genomic: ACTGGACTTGCTCCGGCTCTTCGCCTACGGTACCCTGAATGACTACAAGAgtaagattgt ... gcaagtgtagGTAATTCTGGATTCCTTCCAGCACTGTTGCCTGACCAGGTCCGAAAGCTAA
EST: gi|86472725|gb|DY239095.1|DY239095
EST:     ACTGGACTTGCTCCGGCTCTTCCCCTACGGCACCCTGAATGACTACAAGA                         GTAATTCTGGATTCCTTCCAGCACTGTTGCCTGACCAGGTCCGAAAGCTAA
genomic: ACTGGACTTGCTCCGGCTCTTCGCCTACGGTACCCTGAATGACTACAAGAgtaagattgt ... gcaagtgtagGTAATTCTGGATTCCTTCCAGCACTGTTGCCTGACCAGGTCCGAAAGCTAA
EST: gi|211178519|gb|FK980677.1|FK980677
EST:     ACTGGACTTGCTCCGGCTCTTCGCCTACGGTACCCTGAATGACTACAAGA                         GTAATTCTGGATTCCTTCCAGCACTGTTGCCCTGACCAGGTCCGAAAGCTA
genomic: ACTGGACTTGCTCCGGCTCTTCGCCTACGGTACCCTGAATGACTACAAGAgtaagattgt ... gcaagtgtagGTAATTCTGGATTCCTTCCAGCACTGTTGCC-TGACCAGGTCCGAAAGCTA
EST: gi|211180926|gb|FK980688.1|FK980688
EST:     ACTGGACTTGCTCCGGCTCTTCGCCTACGGTACCCTGAATGACTACAAGA                         GTAATTCTGGATTCCTTCCAGCACTGTTGCCTGACCAGGTCCGAAAGCTAA
genomic: ACTGGACTTGCTCCGGCTCTTCGCCTACGGTACCCTGAATGACTACAAGAgtaagattgt ... gcaagtgtagGTAATTCTGGATTCCTTCCAGCACTGTTGCCTGACCAGGTCCGAAAGCTAA
EST: gi|71427328|gb|DR808378.1|DR808378
EST:     ACTGGACTTGCTCCGGCTCTTCGCCTACGGTACCCTGAATGACTACAAGA                         GTAATTCTGGATTCCTTCCAGCACTGTTGCCTGACCAGGTCCGAAAGCTAA
genomic: ACTGGACTTGCTCCGGCTCTTCGCCTACGGTACCCTGAATGACTACAAGAgtaagattgt ... gcaagtgtagGTAATTCTGGATTCCTTCCAGCACTGTTGCCTGACCAGGTCCGAAAGCTAA
EST: gi|148943925|gb|EC889005.2|EC889005
EST:     ACTGGACTTGCTCCGGCTCTTCGCCTACGGTACCCTGAATGACTACAAGA                         GTAATTCTGGATTCCTTCCAGCACTGTTGCCTGACCAGGTCCGAAAGCTAA
genomic: ACTGGACTTGCTCCGGCTCTTCGCCTACGGTACCCTGAATGACTACAAGAgtaagattgt ... gcaagtgtagGTAATTCTGGATTCCTTCCAGCACTGTTGCCTGACCAGGTCCGAAAGCTAA
EST: gi|148972927|gb|EE023942.2|EE023942
EST:     ACTGGACTTGCTCCGGCTCTTCGCCTACGGTACCCTGAATGACTACAAGA                         GTAATTCTGGATTCCTTCCAGCACTGTTGCCTGACCAGGTCCGAAAGCTAA
genomic: ACTGGACTTGCTCCGGCTCTTCGCCTACGGTACCCTGAATGACTACAAGAgtaagattgt ... gcaagtgtagGTAATTCTGGATTCCTTCCAGCACTGTTGCCTGACCAGGTCCGAAAGCTAA
EST: gi|78081417|gb|DV509829.1|DV509829
EST:     ACTGGACTTGCTCCGGCTCTTCGCCTACGGTACCCTGAATGACTACAAGA                         GTAATTCTGGATTCCTTCCAGCACTGTTGCCTGACCAGGTCCGAAAGCTAA
genomic: ACTGGACTTGCTCCGGCTCTTCGCCTACGGTACCCTGAATGACTACAAGAgtaagattgt ... gcaagtgtagGTAATTCTGGATTCCTTCCAGCACTGTTGCCTGACCAGGTCCGAAAGCTAA
EST: gi|74242379|gb|DT650293.1|DT650293
EST:     ACTGGACTTGCTCCGGCTCTTCGCCTACGGTACCCTGAATGACTACAAGA                         GTAATTCTGGATTCCTTCCAGCACTGTTGCCTGACCAGGTCCGAAAGCTAA
genomic: ACTGGACTTGCTCCGGCTCTTCGCCTACGGTACCCTGAATGACTACAAGAgtaagattgt ... gcaagtgtagGTAATTCTGGATTCCTTCCAGCACTGTTGCCTGACCAGGTCCGAAAGCTAA
EST: gi|211178522|gb|FK980680.1|FK980680
EST:     ACTGGACTTGCTCCGGCTCTTCGCCTACGGTACCCTGAATGACTACAAGA                         GTAATTCTGGATTCCTTCCAGCACTGTTGCCTGACCAGGTCCGAAAGCTAA
genomic: ACTGGACTTGCTCCGGCTCTTCGCCTACGGTACCCTGAATGACTACAAGAgtaagattgt ... gcaagtgtagGTAATTCTGGATTCCTTCCAGCACTGTTGCCTGACCAGGTCCGAAAGCTAA
EST: gi|149089443|gb|EE178684.2|EE178684
EST:     ACTGGACTTGCTCCGGCTCTTCGCCTACGGTACCCTGAATGACTACAAGA                         GTAATTCTGGATTCCTTCCAGCACTGTTGCCTGACCAGGTCCGAAAGCTAA
genomic: ACTGGACTTGCTCCGGCTCTTCGCCTACGGTACCCTGAATGACTACAAGAgtaagattgt ... gcaagtgtagGTAATTCTGGATTCCTTCCAGCACTGTTGCCTGACCAGGTCCGAAAGCTAA
EST: gi|211178525|gb|FK980683.1|FK980683
EST:     ACTGGACTTGCTCCGGCTCTTCGCCTACGGTACCCTGAATGACTACAAGA                         GTAATTCTGGATTCCTTCCAGCACTGTTGCCTGACCAGGTCCGAAAGCTAA
genomic: ACTGGACTTGCTCCGGCTCTTCGCCTACGGTACCCTGAATGACTACAAGAgtaagattgt ... gcaagtgtagGTAATTCTGGATTCCTTCCAGCACTGTTGCCTGACCAGGTCCGAAAGCTAA
EST: gi|76931006|gb|DV172592.1|DV172592
EST:     ACTGGACTTGCTCCGGCTCTTCGCCTACGGTACCCTGAATGACTACAAGA                         GTAATTCTGGATTCCTTCCAGCACTGTTGCCTGACCAGGTCCGAAAGCTAA
genomic: ACTGGACTTGCTCCGGCTCTTCGCCTACGGTACCCTGAATGACTACAAGAgtaagattgt ... gcaagtgtagGTAATTCTGGATTCCTTCCAGCACTGTTGCCTGACCAGGTCCGAAAGCTAA
EST: gi|5268890|gb|AI770854.1|AI770854
EST:     ACTGGACTTGCTCCGGCTCTTCGCCTACGGTACCCTGAATGACTACAAGA                         GTAATTCTGGATTCCTTCCAGCACTGTTGCCTGACCAGGTCCGAAAGCTAA
genomic: ACTGGACTTGCTCCGGCTCTTCGCCTACGGTACCCTGAATGACTACAAGAgtaagattgt ... gcaagtgtagGTAATTCTGGATTCCTTCCAGCACTGTTGCCTGACCAGGTCCGAAAGCTAA
EST: gi|211180929|gb|FK980691.1|FK980691
EST:     ACTGGACTTGCTCCGGCTCTTCGCCTACGGTACCCTGAATGACTACAAGA                         GTAATTCTGGATTCCTTCCAGCACTGTTGCCTGACCAGGTCCGAAAGCTAA
genomic: ACTGGACTTGCTCCGGCTCTTCGCCTACGGTACCCTGAATGACTACAAGAgtaagattgt ... gcaagtgtagGTAATTCTGGATTCCTTCCAGCACTGTTGCCTGACCAGGTCCGAAAGCTAA
EST: gi|211178518|gb|FK980676.1|FK980676
EST:     ACTGGACTTGCTCCGGCTCTTCGCCTACGGTACCCTGAATGACTACAAGA                         GTAATTCTGGATTCCTTCCAGCACTGTTGCCTGACCAGGTCCGAAAGCTAA
genomic: ACTGGACTTGCTCCGGCTCTTCGCCTACGGTACCCTGAATGACTACAAGAgtaagattgt ... gcaagtgtagGTAATTCTGGATTCCTTCCAGCACTGTTGCCTGACCAGGTCCGAAAGCTAA
EST: gi|29129753|gb|CB380457.1|CB380457
EST:     ACTGGACTTGCTCCGGCTCTTCGCCTACGGTACCCTGAATGACTACAAGA                         GTAATTCTGGATTCCTTCCAGCACTGTTGCCTGACCAGGTCCGAAAGCTAA
genomic: ACTGGACTTGCTCCGGCTCTTCGCCTACGGTACCCTGAATGACTACAAGAgtaagattgt ... gcaagtgtagGTAATTCTGGATTCCTTCCAGCACTGTTGCCTGACCAGGTCCGAAAGCTAA
EST: gi|211180931|gb|FK980693.1|FK980693
EST:     ACTGGACTTGCTCCGGCTCTTCGCCTACGGTACCCTGAATGACTACAAGA                         GTAATTCTGGATTCCTTCCAGCACTGTTGCCTGACCAGGTCCGAAAGCTAA
genomic: ACTGGACTTGCTCCGGCTCTTCGCCTACGGTACCCTGAATGACTACAAGAgtaagattgt ... gcaagtgtagGTAATTCTGGATTCCTTCCAGCACTGTTGCCTGACCAGGTCCGAAAGCTAA
EST: gi|78112153|gb|DV530549.1|DV530549
EST:     ACTGGACTTGCTCCGGCTCTTCGCCTACGGTACCCTGAATGACTACAAGA                         GTAATTCTGGATTCCTTCCAGCACTGTTGCCTGACCAGGTCCGAAAGCTAA
genomic: ACTGGACTTGCTCCGGCTCTTCGCCTACGGTACCCTGAATGACTACAAGAgtaagattgt ... gcaagtgtagGTAATTCTGGATTCCTTCCAGCACTGTTGCCTGACCAGGTCCGAAAGCTAA
EST: gi|50339563|gb|CO534689.1|CO534689
EST:     GCGGGACTTGCTCCGGCTCTTCGCCTACGGTACCCTGAATGACTACAAGA                         GTAATTCTGGATTCCTTCCAGCACTGTTGCCTGACCAGGTCCGAAAGCTAA
genomic: ACTGGACTTGCTCCGGCTCTTCGCCTACGGTACCCTGAATGACTACAAGAgtaagattgt ... gcaagtgtagGTAATTCTGGATTCCTTCCAGCACTGTTGCCTGACCAGGTCCGAAAGCTAA
EST: gi|67021495|gb|CO450244.1|CO450244
EST:     ACTGGACTTGCTCCGGCTCTTCGCCTACGGTACCCTGAATGACTACAAGA                         GTAATTCTGGATTCCTTCCAGCACTGTTGCCTGACCAGGTCCGAAAGCTAA
genomic: ACTGGACTTGCTCCGGCTCTTCGCCTACGGTACCCTGAATGACTACAAGAgtaagattgt ... gcaagtgtagGTAATTCTGGATTCCTTCCAGCACTGTTGCCTGACCAGGTCCGAAAGCTAA

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), 49 (downstream exon)
Score: 13

CTCACTGGCACGCAGTACGCGTCGTCACTGGACTTGCTCCGGCTCTTCGCCTACGGTACCCTGAATGACTACAAGAgtaagattgt ... gcaagtgtagGTAATTCTGGATTCCTTCCAGCACTGTTGCCTGACCAGGTCCGAAAGCTAAAGCAGCTCAGCGTGCTAACTCTGGCAGAGTCAACTAAG


Block sizes: 49 (upstream exon), 15 (downstream exon)
Score: 2

CTCACTGGCACGCAGTACGCGTCGTCACTGGACTTGCTCCGGCTCTTCGCCTACGGTACCCTGAATGACTACAAGAgtaagattgt ... gcaagtgtagGTAATTCTGGATTCCTTCCAGCACTGTTGCCTGACCAGGTCCGAAAGCTAAAGCAGCTCAGCGTGCTAACTCTGGCAGAGTCAACTAAG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 6

CTCACTGGCACGCAGTACGCGTCGTCACTGGACTTGCTCCGGCTCTTCGCCTACGGTACCCTGAATGACTACAAGAgtaagattgt ... gcaagtgtagGTAATTCTGGATTCCTTCCAGCACTGTTGCCTGACCAGGTCCGAAAGCTAAAGCAGCTCAGCGTGCTAACTCTGGCAGAGTCAACTAAG


Block sizes: 43 (upstream exon), 29 (downstream exon)
Score: 8

CTCACTGGCACGCAGTACGCGTCGTCACTGGACTTGCTCCGGCTCTTCGCCTACGGTACCCTGAATGACTACAAGAgtaagattgt ... gcaagtgtagGTAATTCTGGATTCCTTCCAGCACTGTTGCCTGACCAGGTCCGAAAGCTAAAGCAGCTCAGCGTGCTAACTCTGGCAGAGTCAACTAAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tatagaaaaatatgcacattgtcttattccttaatgtatctttgtgcaagtgtagGTAATTCTGGATTCCTTCCAGCACTGTTGCCTGACCAGGTCCGAAAGCTAAAGCAGCTCAGCGTGCTAACTCTGGCAGAGTCAACTAAG
                            ccttaat  putative branch site (score: 8)
     aaaaatat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gaattttctgcttgtttgatctaccattgctgtcagcgtgcatattatagaaaaatatgcacattgtcttattccttaatgtatctttgtgcaagtgtagGTAATTCTGGATTCCTTCCAGCACTGTTGCCTGACCAGGTCCGAAAGCTAAAGCAGCTCAGCGTGCTAACTCTGGCAGAGTCAACTAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTCA