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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gtgttacagattgctccatggagtagaagttgcagtcactagccactttgttttttttgacaatgtactgaaataatttgggttttgtgcacttctgcagAATCATCCTGGAAACAGATGCAAACACCATTGCTGGTAAGGTTGCAACCAATGCTGTTGATGGTTCTGTGCCCTTTTCTGAGCAG

Basic information

species Zea mays
transcript GRMZM2G314679_T06
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G314679_T02 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os02g21250.1 (Oryza sativa), 3'ss of exon 5
gtgttacagattgctccatggagtagaagttgcag-tcactagccactttgttttttttgacaatgtactg-----aaat---aatttgggttttgtgcacttctgcagAATCATCCTGGAAACAGATGCAAACACCATTGCTGGTAAGGTTGCAACCAATGCTGTTGATGGTTCTGTGCCCTTTTCTGAGCAG
        |     | |||| | || | |  |||| || || |  |   |||  |||   |     | |||     ||||   || |       |  |  || |||||| || || ||||||||||||||||| |||||||| || |||||||||||||||||||||||||||||||  ||||| |||||||||
--------gccaatttcatgtatta-aggccgcagctctcttgtgaagctgtagtttcacatgccatcctgtttgtaaatataaactgaaaccattagtcctcctgcagCATAATTCTGGAAACAGATGCAAATACCATTGCCGGGAAGGTTGCAACCAATGCTGTTGATGGTTCTGCCCCCTTCTCTGAGCAG
















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|211411155|gb|FK961654.1|FK961654
EST:     GAGAACTTGGATTTGATACTTCTCTGCATTGATGAAATTGTGGATGGGGG                         AATCATCCTGGAAACAGATGCAAACACCATTGCTGGTAAGGTTGCAACCAA
genomic: GAGAACTTGGATTTGATACTTCTCTGCATTGATGAAATTGTGGATGGGGGgtaacaatct ... acttctgcagAATCATCCTGGAAACAGATGCAAACACCATTGCTGGTAAGGTTGCAACCAA
EST: gi|60356728|gb|DN223701.1|DN223701
EST:     GAGAACTTGGATTTGATACTTCTCTGCATTGATGAAATTGTAGATGGGGG                         AATCATCCTGGAAACAGATGCAAACACCATTGCTGGTAAGGTTGCAACCAA
genomic: GAGAACTTGGATTTGATACTTCTCTGCATTGATGAAATTGTGGATGGGGGgtaacaatct ... acttctgcagAATCATCCTGGAAACAGATGCAAACACCATTGCTGGTAAGGTTGCAACCAA
EST: gi|32849532|gb|CD989213.1|CD989213
EST:     GAGAACTTGGATTTGATACTTCTCTGCATTGATGAAATTGTGGATGGGGG                         AATCATCCTGGAAACAGATGCAAACACCATTGCTGGTAAGGTTGCAACCAA
genomic: GAGAACTTGGATTTGATACTTCTCTGCATTGATGAAATTGTGGATGGGGGgtaacaatct ... acttctgcagAATCATCCTGGAAACAGATGCAAACACCATTGCTGGTAAGGTTGCAACCAA
EST: gi|15323565|gb|BI478787.1|BI478787
EST:     GAGAACTTGGATTTGATACTTCTCTGCATTGATGAAATTGTAGATGGGGG                         AATCATCCTGGAAACAGATGCAAACACCATTGCTGGTAAGGTTGCAACCAA
genomic: GAGAACTTGGATTTGATACTTCTCTGCATTGATGAAATTGTGGATGGGGGgtaacaatct ... acttctgcagAATCATCCTGGAAACAGATGCAAACACCATTGCTGGTAAGGTTGCAACCAA
EST: gi|4681229|gb|AI629899.1|AI629899
EST:     GAGAACTTGGATTTGATACTTCTCTGCATTGATGAAATTGTGGATGGGGG                         AATCATCCTGGAAACAGATGCAAACACCATTGCTGGTAAGGTTGCAACCAA
genomic: GAGAACTTGGATTTGATACTTCTCTGCATTGATGAAATTGTGGATGGGGGgtaacaatct ... acttctgcagAATCATCCTGGAAACAGATGCAAACACCATTGCTGGTAAGGTTGCAACCAA
EST: gi|32908218|gb|CF013031.1|CF013031
EST:     GAGAACTTGGATTTGATACTTCTCTGCATTGATGAAATTGTGGATGGGGG                         AATCATCCTGGAAACAGATGCAAACACCATTGCTGGTAAGGTTGCAACCAA
genomic: GAGAACTTGGATTTGATACTTCTCTGCATTGATGAAATTGTGGATGGGGGgtaacaatct ... acttctgcagAATCATCCTGGAAACAGATGCAAACACCATTGCTGGTAAGGTTGCAACCAA
EST: gi|32938645|gb|CF043464.1|CF043464
EST:     GAGAACTTGGATTTGATACTTCTCTGCATTGATGAAATTGTGGATGGGGG                         AATCATCCTGGAAACAGATGCAAACACCATTGCTGGTAAGGTTGCAACCAA
genomic: GAGAACTTGGATTTGATACTTCTCTGCATTGATGAAATTGTGGATGGGGGgtaacaatct ... acttctgcagAATCATCCTGGAAACAGATGCAAACACCATTGCTGGTAAGGTTGCAACCAA
EST: gi|4646698|gb|AI491558.2|AI491558
EST:     GAGAACTTGGATTTGATACTTCTCTGCATTGATGAAATTGTGGATGGGGG                         AATCATCCTGGAAACAGATGCAAACCCCATCGCTGGTAAGGATGCAACCAA
genomic: GAGAACTTGGATTTGATACTTCTCTGCATTGATGAAATTGTGGATGGGGGgtaacaatct ... acttctgcagAATCATCCTGGAAACAGATGCAAACACCATTGCTGGTAAGGTTGCAACCAA
EST: gi|5296305|gb|AI783075.1|AI783075
EST:     GAGAACTTGGATTTGATACTTCTCTGCATCGATGAAATTGTAGATGGGGG                         AATCATCCTGGAAACAGATGCAAACACCATTGCTGGTAAGGTTGCAACCAA
genomic: GAGAACTTGGATTTGATACTTCTCTGCATTGATGAAATTGTGGATGGGGGgtaacaatct ... acttctgcagAATCATCCTGGAAACAGATGCAAACACCATTGCTGGTAAGGTTGCAACCAA
EST: gi|91873753|gb|EB403710.1|EB403710
EST:     GAGAACTTGGATTTGATACTTCTCTGCATTGATGAAATTGTGGATGGGGG                         AATCATCCTGGAAACAGATGCAAACACCATTGCTGGTAAGGTTGCAACCAA
genomic: GAGAACTTGGATTTGATACTTCTCTGCATTGATGAAATTGTGGATGGGGGgtaacaatct ... acttctgcagAATCATCCTGGAAACAGATGCAAACACCATTGCTGGTAAGGTTGCAACCAA
EST: gi|5901227|gb|AW042327.1|AW042327
EST:     GAGAACTTGGATTTGATACTTCTCTGCATCGATGAAATTGTAGATGGGGG                         AATCATCCTGGAAACAGATGCAAACACCATTGCTGGTAAGGTTGCAACCAA
genomic: GAGAACTTGGATTTGATACTTCTCTGCATTGATGAAATTGTGGATGGGGGgtaacaatct ... acttctgcagAATCATCCTGGAAACAGATGCAAACACCATTGCTGGTAAGGTTGCAACCAA
EST: gi|16925380|gb|BM078448.1|BM078448
EST:     GAGAACTTGGATTTGATACTTCTCTGCATTGATGAAATTGTGGATGGGGG                         AATCATCCTGGAAACAGATGCAAACACCATTGCTGGTAAGGTTGCAACCAA
genomic: GAGAACTTGGATTTGATACTTCTCTGCATTGATGAAATTGTGGATGGGGGgtaacaatct ... acttctgcagAATCATCCTGGAAACAGATGCAAACACCATTGCTGGTAAGGTTGCAACCAA
EST: gi|6227104|gb|AW155808.1|AW155808
EST:     GAGAACTTGGATTTGATACTTCTCTGCATCGATGAAATTGTAGATGGGGG                         AATCATCCTGGAAACAGATGCAAACACCATTGCTGNTAAGGTTGCAACCAA
genomic: GAGAACTTGGATTTGATACTTCTCTGCATTGATGAAATTGTGGATGGGGGgtaacaatct ... acttctgcagAATCATCCTGGAAACAGATGCAAACACCATTGCTGGTAAGGTTGCAACCAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctttgttttttttgacaatgtactgaaataatttgggttttgtgcacttctgcagAATCATCCTGGAAACAGATGCAAACACCATTGCTGGTAAGGTTGCAACCAATGCTGTTGATGGTTCTGTGCCCTTTTCTGAGCAG
         ttttgac  putative branch site (score: 3)
                                            cacttct  putative PPT
     ttttttttgacaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgttacagattgctccatggagtagaagttgcagtcactagccactttgttttttttgacaatgtactgaaataatttgggttttgtgcacttctgcagAATCATCCTGGAAACAGATGCAAACACCATTGCTGGTAAGGTTGCAACCAATGCTGTTGATGGTTCTGTGCCCTTTTCTGAGCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGCAG