RetrogeneDB ID: retro_cfam_1600

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 36:11616978..11617457(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: None
• Aliases: None
• Status: NOVEL

Parental gene information

• Parental gene symbol: TSPAN6
• Ensembl ID: ENSCAFG00000017521
• Aliases: None
• Description: tetraspanin 6 [Source:HGNC Symbol;Acc:11858]

Sequence

>retro_cfam_1600
GCGCCTGGTGCGGTTGGTGCAGGGTCGTGGGCTACTCATGGCGTCCCCGTCTCAGAGACTGCAGACCAAACCAGTCATTA
CTTGTTTCAAGAGCGCCTCTTGATCTACACTTTCATCTTCTGGATCACTGGCGTAATCCTTCTTGCCATTGGCATTTGGG
GCAAGGTGAGCCTGGAGAATTATTTTTCCCTTTTAAATGAGAAGGCCACCAATGTCCCCTTCATGCTCATTGGCACTGGC
ACTGTCATCATTCTTTTGGGCACCTTTGGCTGTTTTGCTACCTGCCGAGCTTCTGCATGGATGCTAAAACTTACGCAATG
TTTCTGACTCTCATTTTTTTGGTTGAATTGGTTGCTGCCATCATAGAATTTGTTTTCATGCATGAGATTAGGAATAGCTT
TAAGAATAATTATGAGAAAATTTTAAAGCAGTATAACTCTATGGGAGATTATAGAAGCGATGCAGTAGACAAGATTAGA

Alignment

ORF - retro_cfam_1600 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 88.96 %
• Parental protein coverage: 56.18 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  APGAVG-QGRGV-MASPSRRLQTKPVITCFKSV-LLIYTFIFWITGLILLAVGIWGKVSLENYFSLLNEK
          APGAVG.QGRG..MASPS.RLQTKPVITCFKS..LLIYTFIFWITG.ILLA.GIWGKVSLENYFSLLNEK
Retrocopy APGAVG>QGRGLLMASPSQRLQTKPVITCFKSA<LLIYTFIFWITGVILLAIGIWGKVSLENYFSLLNEK

Parental  ATNVPFVLIGTGTVIILLGTFGCFATCRASAWMLKL-YAMFLTLIFLVELVAAIVGFVFRHEIRNSFKSN
          ATNVPF.LIGTGTVIILLGTFGCFATCRASAWMLKL.YAMFLTLIFLVELVAAI..FVF.HEIRNSFK.N
Retrocopy ATNVPFMLIGTGTVIILLGTFGCFATCRASAWMLKL<YAMFLTLIFLVELVAAIIEFVFMHEIRNSFKNN

Parental  YERTLKQYNSTGDYRSDAVDKIQ
          YE..LKQYNS.GDYRSDAVDKI.
Retrocopy YEKILKQYNSMGDYRSDAVDKIR

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	0.00 RPM	16.51 RPM
SRP017611_brain	0.00 RPM	8.89 RPM
SRP017611_kidney	0.00 RPM	55.34 RPM
SRP017611_liver	0.00 RPM	7.90 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_1600 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_1600 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_1600 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 10 parental genes, and 13 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000017521	3 retrocopies	retro_cfam_1600 , retro_cfam_1609, retro_cfam_878,
Canis familiaris	ENSCAFG00000018068	2 retrocopies	retro_cfam_1391, retro_cfam_571,
Callithrix jacchus	ENSCJAG00000004288	1 retrocopy	retro_cjac_2306,
Echinops telfairi	ENSETEG00000012276	1 retrocopy	retro_etel_1987,
Loxodonta africana	ENSLAFG00000027296	1 retrocopy	retro_lafr_994,
Microcebus murinus	ENSMICG00000011370	1 retrocopy	retro_mmur_447,
Nomascus leucogenys	ENSNLEG00000007505	1 retrocopy	retro_nleu_1186,
Otolemur garnettii	ENSOGAG00000004869	1 retrocopy	retro_ogar_2827,
Sarcophilus harrisii	ENSSHAG00000000274	1 retrocopy	retro_shar_515,
Sus scrofa	ENSSSCG00000012481	1 retrocopy	retro_sscr_84,