RetrogeneDB ID: retro_cfam_878

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 19:43215314..43216051(-)
• Located in intron of: ENSCAFG00000005403

Retrocopy information

• Ensembl ID: ENSCAFG00000031531
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

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

Sequence

>retro_cfam_878
GTCATGGAGTCCCCGTCTCGGAGACTGAAGACGAAACCAGTCATTACTTGTTTCAAGAGCATCCTCTTGATCTACACTTT
CATCTTCTGGATCACTGGCCTAATCCTTCTTGCCGTTGGCATTTGGGGCAAGGTGAGCCTGGAGAATTATGTTTCCCTTT
TAAATGAGAAGGCCACCAATGTCCCCTTCGTGGTCATTGGCACTGGCACTGTCATCATTCTTTTGGGCACCTTTGGCTGT
TTTGCTACCTGCCGAGCTTCTGCATGGATGCTAAAACTGTATGCAATGTTTCTGACTCTCATTTTTTTGGTTGAATTGGT
CACTGCCATCTTAGGATTTGTTTTCAGACATGAGATTAGGAACAGCTTTAAGAATAATTATGAGAAAACTTTAAAGCAGT
ATAACTCTACGGGAGATTATAGAAGCGATGCAGTAGACAAGATTCAAAATACGTTACCTTGTTGTGGTGTCACCGACTAT
AGAGATTGAGGGATACTAATTATTACTCAGAAAAAGGATTTCCCAAGAGTTGCTGTAAACTTGAAAATTGTTCTCCACAG
AGAGATGCAGATAAAGTAAACAATGAAGGTTGTTTTATAAAGGTGATGACCATTATAGAGTCAGAAATGGGAGTGGTTGC
GGGAATTTCTTTTGGAGTTGCTTGCTTTCAGCTGGTTGGAATCTTTCTATCCTACTGCCTCTCTTGCGCCATAACAAATA
ACCAGTATGAGATAGTG

Alignment

ORF - retro_cfam_878 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 94.74 %
• Parental protein coverage: 86.93 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  VMASPSRRLQTKPVITCFKSVLLIYTFIFWITGLILLAVGIWGKVSLENYFSLLNEKATNVPFVLIGTGT
          VM.SPSRRL.TKPVITCFKS.LLIYTFIFWITGLILLAVGIWGKVSLENY.SLLNEKATNVPFV.IGTGT
Retrocopy VMESPSRRLKTKPVITCFKSILLIYTFIFWITGLILLAVGIWGKVSLENYVSLLNEKATNVPFVVIGTGT

Parental  VIILLGTFGCFATCRASAWMLKLYAMFLTLIFLVELVAAIVGFVFRHEIRNSFKSNYERTLKQYNSTGDY
          VIILLGTFGCFATCRASAWMLKLYAMFLTLIFLVELV.AI.GFVFRHEIRNSFK.NYE.TLKQYNSTGDY
Retrocopy VIILLGTFGCFATCRASAWMLKLYAMFLTLIFLVELVTAILGFVFRHEIRNSFKNNYEKTLKQYNSTGDY

Parental  RSDAVDKIQNTLHCCGVTDYRD-WRDTNYYSEKGFPKSCCKLENCSPQRDADKVNNEGCFIKVMTIIESE
          RSDAVDKIQNTL.CCGVTDYRD..RDTNYYSEKGFPKSCCKLENCSPQRDADKVNNEGCFIKVMTIIESE
Retrocopy RSDAVDKIQNTLPCCGVTDYRD<LRDTNYYSEKGFPKSCCKLENCSPQRDADKVNNEGCFIKVMTIIESE

Parental  MGVVAGISFGVACFQLVGIFLSYCLSRAITNNQYEIV
          MGVVAGISFGVACFQLVGIFLSYCLS.AITNNQYEIV
Retrocopy MGVVAGISFGVACFQLVGIFLSYCLSCAITNNQYEIV

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	0.76 RPM	16.51 RPM
SRP017611_brain	0.40 RPM	8.89 RPM
SRP017611_kidney	3.24 RPM	55.34 RPM
SRP017611_liver	0.29 RPM	7.90 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_878 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_878 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_878 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,