RetrogeneDB ID: retro_cfam_1609

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 37:14915654..14916413(+)
• 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_1609
GCAGTGGGGCAGGGTCGTGGGCTAGTCATGGTGTCCCCGTCTGGGAGGCTGCAGACCAAACCAGTCATTACTTGTTTCAA
GAGCATCCTCTTGATCTACACTTTCATCTTCTGGATCACTGGTGTAATCCTTCTTGCCGTTGGCATTTGGGACAAGATGA
GCCTGGAGAATTATTTTTCCTTTTAAATAAGAAGGTCACCAATGTCCCCTTTGTGCTCATTGGCACTGGCACTGTCATCA
TGCTTTTGGGCACCTTTGGCTGTTTTGCTACCTGCCGAGCTTTTGCATGGATGCTAAAACTGTATGCAATGTTTCTGACT
CTCATTTTTTTGGTTGAATTGGTCGCTGCCATCGTAGGATTTGTTTTCAGGCATGAGATAAGGAACAGCTTTTAGAATAA
TTATGAGAAAACTTTAAAGCAGTATAACTCTATGGGAGATTATAGAAGCGATGCAGTAGACAAGATTCAAAATATGTTAC
ATCGTGTGGTGTCACCGACTATTGAGATTGGAGGGATACTGATTATTACTCAGAAAAAGGATTTCCCAAGAGTTGCTGTA
AACTTGAAAATGGTTCTCCAAGAGAGATGCAGATAAAGTAAACAATGAAAGTTGTTTTATAAAGGTGATGACCATTAAAG
AGTCAGAAATGGGAATGGTTGTGGGAATTTCTTTTGGAGTTGCTTGCTTTCAGCTGGTTGGAATCCTTCTAGCCTACTGC
CTCTCTCGCGCCATAACGAATAACCAGTATGAGATAGTG

Alignment

ORF - retro_cfam_1609 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 88.33 %
• Parental protein coverage: 89.4 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  AVGQGRG-VMASPSRRLQTKPVITCFKSVLLIYTFIFWITGLILLAVGIWGKVSLENYFS-LLNEKATNV
          AVGQGRG.VM.SPS.RLQTKPVITCFKS.LLIYTFIFWITG.ILLAVGIW.K.SLENYFS.LLN.K.TNV
Retrocopy AVGQGRGLVMVSPSGRLQTKPVITCFKSILLIYTFIFWITGVILLAVGIWDKMSLENYFS<LLNKKVTNV

Parental  PFVLIGTGTVIILLGTFGCFATCRASAWMLKLYAMFLTLIFLVELVAAIVGFVFRHEIRNSFKSNYERTL
          PFVLIGTGTVI.LLGTFGCFATCRA.AWMLKLYAMFLTLIFLVELVAAIVGFVFRHEIRNSF..NYE.TL
Retrocopy PFVLIGTGTVIMLLGTFGCFATCRAFAWMLKLYAMFLTLIFLVELVAAIVGFVFRHEIRNSF*NNYEKTL

Parental  KQYNSTGDYRSDAVDKIQNTLH-CCGVTDYRDWRDTNYYSEKGFPKSCCKLENCSP-QRDADKVNNEGCF
          KQYNS.GDYRSDAVDKIQN.LH..CGVTDY.DWRDT.YYSEKGFPKSCCKLEN.SP..RDADKVNNE.CF
Retrocopy KQYNSMGDYRSDAVDKIQNMLH<SCGVTDY*DWRDTDYYSEKGFPKSCCKLENGSP<KRDADKVNNESCF

Parental  IKVMTIIESEMGVVAGISFGVACFQLVGIFLSYCLSRAITNNQYEIV
          IKVMTI.ESEMG.V.GISFGVACFQLVGI.L.YCLSRAITNNQYEIV
Retrocopy IKVMTIKESEMGMVVGISFGVACFQLVGILLAYCLSRAITNNQYEIV

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_1609 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_1609 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_1609 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,