RetrogeneDB ID: retro_cfam_736

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 16:34232131..34233026(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCAFG00000006566
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: PINX1
• Ensembl ID: ENSCAFG00000008087
• Aliases: None
• Description: PIN2/TERF1 interacting, telomerase inhibitor 1 [Source:HGNC Symbol;Acc:30046]

Sequence

>retro_cfam_736
TCTATGCTGGCTGAGCATCAGAGGAAGCAGAAGTGGGCTGTGGATCCAAGAAACACTGCGTGGAGCAATGATGATTCCAA
GTTTGGCCAGAGGATGCTAGAAAAAATGGGGTGGTCTAAAGGAAAGGGTTTAGGGGCTCAGGAGCAAGGAGCAACAGATC
ATATTAAAGTTCAAGTTAAAAATAACCACCTGGGACTTGGAGCTACAATCAATAATGAAGATAACTGGATTGCTCATCAG
GATGATTTTAACCAGCTTTTGGCTGACCTGAACACTTGCCATGGGCAGGAAACAACAGATTCCTCACACAACAAAGAGAA
GAAAACTTTCAGCCTCGAAGAAAAGTCCAAAATCTCCAAAAAACAGTGTTCATTATATGAAATTCACAAAAGGGAATGAT
CTATCATGTCGGAGCAAAACAGATCTTGACTACATTTTTGGAAAAAGACAGAGTAAGAAGATTCCTGAGGATGATTCCAG
CCCTGCCACTCCAGATGGGAACTCATCCTCCACTACAACGACCAGTGCCTTCACCATCCAGGAGTACTTTGCCAAGAGGA
AGGCAGAGCTAAAGAACAAGCCACAGGTCATAGCAGCAGGGCCTGACTTTGCAGAGACCCAAACAGAAAGAAAAAATGGA
AAGAAAAGAAAGAAAGAGGCAAAAGATAGAAAAGTGGAGATATACACCGTACCCAAGGCCAAGAAGAAGAGACACCAAGT
TGAGTGGCAGCTTGGAGACCCTTGTTGGGACAAGAATTCTGGTGTTTCTGCTGAAAATGGAGAAGATTGTGTGTGGCCAC
CTCATGTCCAGGACATTACCCTAAAGTCCAAGAAAAGGAGAGAAAAGAAAAACCAAGTTGAAGTAGCTATGGACGCTACA
TTACATGACACACCT

Alignment

ORF - retro_cfam_736 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 88.08 %
• Parental protein coverage: 96.78 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  TLLFTGRRKQKWAVDPRNTAWSNDDSKFGQRMLEKMGWSKGKGLGAQEQGATDHIKVQVKNNHLGLGATI
          ..L....RKQKWAVDPRNTAWSNDDSKFGQRMLEKMGWSKGKGLGAQEQGATDHIKVQVKNNHLGLGATI
Retrocopy SMLAEHQRKQKWAVDPRNTAWSNDDSKFGQRMLEKMGWSKGKGLGAQEQGATDHIKVQVKNNHLGLGATI

Parental  NNEDNWIAHQDDFNQLLADLNTCHGQETTDSSDNKEKKTFSLEEKSKISK-NRVHYMKFTKGKDLSCRSK
          NNEDNWIAHQDDFNQLLADLNTCHGQETTDSS.NKEKKTFSLEEKSKISK.N.VHYMKFTKG.DLSCRSK
Retrocopy NNEDNWIAHQDDFNQLLADLNTCHGQETTDSSHNKEKKTFSLEEKSKISK>NSVHYMKFTKGNDLSCRSK

Parental  TDLDCIFGKRQSKKTPEDDSSPATPDGNSSSTTTTSAFTIQEYFAKRMAELKNKPQVIAAGPDFAETQME
          TDLD.IFGKRQSKK.PEDDSSPATPDGNSSSTTTTSAFTIQEYFAKR.AELKNKPQVIAAGPDFAETQ..
Retrocopy TDLDYIFGKRQSKKIPEDDSSPATPDGNSSSTTTTSAFTIQEYFAKRKAELKNKPQVIAAGPDFAETQXX

Parental  RKNGKKRKKEAKDRKVETYTVPKAKKKRHQVEWQLGDPCWDKNSGVSAENGEDCVWPPHVQDITLKSKKR
          ................E.YTVPKAKKKRHQVEWQLGDPCWDKNSGVSAENGEDCVWPPHVQDITLKSKKR
Retrocopy XXXXXXXXXXXXXXXXEIYTVPKAKKKRHQVEWQLGDPCWDKNSGVSAENGEDCVWPPHVQDITLKSKKR

Parental  REKKKLQNQVEVAIDATLHDTP
          REKK...NQVEVA.DATLHDTP
Retrocopy REKK---NQVEVAMDATLHDTP

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	0.13 RPM	4.20 RPM
SRP017611_brain	0.00 RPM	2.46 RPM
SRP017611_kidney	0.07 RPM	7.66 RPM
SRP017611_liver	0.07 RPM	2.76 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_736 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_736 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_736 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 3 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000008087	1 retrocopy	retro_cfam_736 ,
Homo sapiens	ENSG00000254093	1 retrocopy	retro_hsap_3644,
Pan troglodytes	ENSPTRG00000019980	1 retrocopy	retro_ptro_2469,