RetrogeneDB ID: retro_cfam_1523

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 33:16957954..16959433(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCAFG00000010477
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: MTMR12
• Ensembl ID: ENSCAFG00000018909
• Aliases: None
• Description: myotubularin related protein 12 [Source:HGNC Symbol;Acc:18191]

Sequence

>retro_cfam_1523
GAAATTCATGCAAACGAGAAGGAAGTAACTCTTCACTTGTTGCCAGGTGAACAGCTGCTTTGTGAAGCCAGTACAGTGCT
GAAGTATGTCCAGGAGGATTCCTGTCAGCGTGGGATCTATGGGAAACTTGTGTGCACAGACTTCAAGATCGCCTTCTTGG
GCGATGATGAATCTGCGTTGGATAATGATGAGGCCCAATTTAAGAATAAGGTTATAGGAGAAAATGACATCACACTCCAC
TGCGTTGATCAGATTTATGGAGTGTTTGATGAGAAAAAGAAACCTCTTTTTGGACAATTGAAGAAATACCCTGAAAAACT
CATCATCCACTGCAAAGACCTTCGAGTGTTCCACTTTGGTCTGAGGTACACAAGAGAAGAGGAAGTCAAAAGGATTGTCA
GTGGCATAATTCATCATACCCAAGCTCCTAAACTGCTTAAAAGATTATTTCTGTTTTCCTATGCAGCTGCTGCACAAAAC
AATACAGCCACTGATCCCAAGAACCATACTGTAATGTTTGACACCCTTAAGGACTGGTGTTGGGAATTGGAGCGGACCAA
AGGCAACGTCAAGTACAAAGCAGTGAGTGTCAATGAAGGCTATAAAGTCTGTGTAAGATTGCCAGCATACTTTGTTGTCC
CTATTTCTCTTCCTGAAGAGGACGTGCTACGCTTTCAGGGTCACGGCATACCAATATGGTGCTGGTCCTGCCACAATGGA
TGTGCCCTTTTGAAAATGTCAGCACTGCCCAAAGAACAGGATGATGGCAGTTTACAAATCCAAAAGAGCTTCTTGGATGG
AATTTACAAGACCATCCACAGGCCACCCTATGAAATTGTTAAAACTGAAGACCTGTCAACCAACTTCCTGTCCTTGCAGG
ACATCCAGACTGCATACTCTAAATTTAAACAGCTGTTTCTGATAGATAATAGTACGGAATTTTGGGACACAGATATAAAA
TGGTTTTCTCTGTTGGAAAATAGCAGTTGGCTTGATATAATCAGACGTTGCCTGAAAAAAGCAATAGAGATTGCAGAATG
TCTAGAAGCACAAAACATGAACGTTCTTCTTTTAGAGGAGAATGCTTCAGACCTCTGCTGCCTCATTTCCTCTCTGGTAC
AAGTGATGATGGACCCCCACTGCAGAACCAGGGTTGGTTTCCAGAGCCTCGTCCAGAAGGAGTGGATCATGGGCGGCCAC
TGTTTCCTGGATCGCTGCAACCACCTCCGTCAAAGTGACAAAGAGGAGGTTCCCGTGTTCCTGCTGTTCTTAGATTGTGT
GTGGCAGCTGGTGCACCAGCATCCCCCAGCATTTGATTTCACGGAGACTTACTTGACTGTTTTGTCAGATAGTCTATACT
TACCTATTTTTAGCACCTTCTTCTTCAATTCGCCTCATCAAAAAGATATTAACATGGGTAGGGAACACCAGGATACACAG
AGCAAGCCTTTGAATCTGCTCACCGTGTGGGATTGGAAC

Alignment

ORF - retro_cfam_1523 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 98.78 %
• Parental protein coverage: 68.47 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  EKEVTEKEVTLHLLPGEQLLCEASTVLKYVQEDSCQRGIYGKLVCTDFKIAFLGDDESALDNDEAQFKNK
          E....EKEVTLHLLPGEQLLCEASTVLKYVQEDSCQRGIYGKLVCTDFKIAFLGDDESALDNDEAQFKNK
Retrocopy EIHANEKEVTLHLLPGEQLLCEASTVLKYVQEDSCQRGIYGKLVCTDFKIAFLGDDESALDNDEAQFKNK

Parental  VIGENDITLHCVDQIYGVFDEKKKPLFGQLKKYPEKLIIHCKDLRVFHFGLRYTKEEEVKRIVSGIIHHT
          VIGENDITLHCVDQIYGVFDEKKKPLFGQLKKYPEKLIIHCKDLRVFHFGLRYT.EEEVKRIVSGIIHHT
Retrocopy VIGENDITLHCVDQIYGVFDEKKKPLFGQLKKYPEKLIIHCKDLRVFHFGLRYTREEEVKRIVSGIIHHT

Parental  QAPKLLKRLFLFSYAAAAQNNTATDPKNHTVMFDTLKDWCWELERTKGNVKYKAVSVNEGYKVCVRLPAY
          QAPKLLKRLFLFSYAAAAQNNTATDPKNHTVMFDTLKDWCWELERTKGNVKYKAVSVNEGYKVCVRLPAY
Retrocopy QAPKLLKRLFLFSYAAAAQNNTATDPKNHTVMFDTLKDWCWELERTKGNVKYKAVSVNEGYKVCVRLPAY

Parental  FVVPISLPEEDVLRFQGHGIPIWCWSCHNGCALLKMSALPKEQDDGSLQIQKSFLDGIYKTIHRPPYEIV
          FVVPISLPEEDVLRFQGHGIPIWCWSCHNGCALLKMSALPKEQDDGSLQIQKSFLDGIYKTIHRPPYEIV
Retrocopy FVVPISLPEEDVLRFQGHGIPIWCWSCHNGCALLKMSALPKEQDDGSLQIQKSFLDGIYKTIHRPPYEIV

Parental  KTEDLSTNFLSLQDIQTAYSKFKQLFLIDNSTEFWDTDIKWFSLLENSSWLDIIRRCLKKAIEIAECLEA
          KTEDLSTNFLSLQDIQTAYSKFKQLFLIDNSTEFWDTDIKWFSLLENSSWLDIIRRCLKKAIEIAECLEA
Retrocopy KTEDLSTNFLSLQDIQTAYSKFKQLFLIDNSTEFWDTDIKWFSLLENSSWLDIIRRCLKKAIEIAECLEA

Parental  QNMNVLLLEENASDLCCLISSLVQVMMDPHCRTRVGFQSLVQKEWIMGGHCFLDRCNHLRQSDKEEVPVF
          QNMNVLLLEENASDLCCLISSLVQVMMDPHCRTRVGFQSLVQKEWIMGGHCFLDRCNHLRQSDKEEVPVF
Retrocopy QNMNVLLLEENASDLCCLISSLVQVMMDPHCRTRVGFQSLVQKEWIMGGHCFLDRCNHLRQSDKEEVPVF

Parental  LLFLDCVWQLVHQHPPAFDFTETYLTVLSDSLYLPIFSTFFFNSPHQKDINMGREHQDTQSKPLNLLTVW
          LLFLDCVWQLVHQHPPAFDFTETYLTVLSDSLYLPIFSTFFFNSPHQKDINMGREHQDTQSKPLNLLTVW
Retrocopy LLFLDCVWQLVHQHPPAFDFTETYLTVLSDSLYLPIFSTFFFNSPHQKDINMGREHQDTQSKPLNLLTVW

Parental  DWS
          DW.
Retrocopy DWN

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Expression validation based on RNA-Seq data:

Library	Retrocopy expression	Parental gene expression
SRP012049_cerebellum	0.42 RPM	8.90 RPM
SRP017611_brain	0.79 RPM	9.61 RPM
SRP017611_kidney	0.73 RPM	7.92 RPM
SRP017611_liver	0.07 RPM	0.65 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_1523 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_1523 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_1523 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 2 parental genes, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000018909	1 retrocopy	retro_cfam_1523 ,
Microcebus murinus	ENSMICG00000002269	1 retrocopy	retro_mmur_630,