RetrogeneDB ID: retro_cfam_1391

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 3:83553255..83553957(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCAFG00000016350
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: TSPAN3
• Ensembl ID: ENSCAFG00000018068
• Aliases: None
• Description: tetraspanin 3 [Source:HGNC Symbol;Acc:17752]

Sequence

>retro_cfam_1391
TTCTGGGGGGCACCTGGCATTTTATGTTATGTGGGAGCCTATGTCTTTATCACTTACGAGGACTATGACCACTTCTTTGA
AGATGTGCGTACTCTCCTTCCCGCTGTAGTGACCATAGCTGTAGGAGCCCCGCTTTTCATTATTGGCCTAATTGGCTGCT
GTGCCACAGTCCGAGAAAGCCGCTGTGGACTTGCCACGTTTGTCATCATCCTACTCTTGGTTTTTGTCACAGAAGTTGTT
GTTGTGGTTTTGGGATACGTTTACAGAGCAAAGGTGGAAACTGAGGTCGATCGCAGCATTCAGAAAGTGTATAAGACCTA
CAATGGAACCAACCCTGATGCTGCTAGCCGGGCTGTTGATTATGTACAGAGACAGCTGCATTGTTGTGGAATTCACAACT
ATTCAGACTGGGAAAATACAGACTGGTTCAAAGAAACCAAAAACCAGAGTGTCCCTCTTAGCTGCTGCACAGAGACCGCC
AGCAGCTGTAATGGCAGCCTGGCCCACCCCTCCAACCTCTATGCCGAGGGATGTGAGGCTCTAGTTGTAAAGAAGCTACA
GGAAATCATGATGCATGTTATCTGGGCAGCGCTGGCATTTGCAGCTATTCAGCTGCTGGGCATGTTATGTGCATGCATCG
TATTGTGCAGAAGGAGTAGAGACCCTGCTTATGAGCTCCTCATCACCGGTGGAACGTACGCA

Alignment

ORF - retro_cfam_1391 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 95.32 %
• Parental protein coverage: 93.63 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  FWKGAAGILCYVGAYVFITYDDYDHFFEDVYTLIPAVVIIAVGALLFIIGLIGCCATIRESRCGLATFVI
          FW.GA.GILCYVGAYVFITY.DYDHFFEDV.TL.PAVV.IAVGA.LFIIGLIGCCAT.RESRCGLATFVI
Retrocopy FW-GAPGILCYVGAYVFITYEDYDHFFEDVRTLLPAVVTIAVGAPLFIIGLIGCCATVRESRCGLATFVI

Parental  ILLLVFVTEVVVVVLGYVYRAKVENEVDRSIQKVYKTYNGTNPDAASRAIDYVQRQLHCCGIHNYSDWEN
          ILLLVFVTEVVVVVLGYVYRAKVE.EVDRSIQKVYKTYNGTNPDAASRA.DYVQRQLHCCGIHNYSDWEN
Retrocopy ILLLVFVTEVVVVVLGYVYRAKVETEVDRSIQKVYKTYNGTNPDAASRAVDYVQRQLHCCGIHNYSDWEN

Parental  TDWFKETKNQSVPLSCCRETASSCNGSLAHPSNLYAEGCEALVVKKLQEIMMHVIWAALAFAAIQLLGML
          TDWFKETKNQSVPLSCC.ETASSCNGSLAHPSNLYAEGCEALVVKKLQEIMMHVIWAALAFAAIQLLGML
Retrocopy TDWFKETKNQSVPLSCCTETASSCNGSLAHPSNLYAEGCEALVVKKLQEIMMHVIWAALAFAAIQLLGML

Parental  CACIVLCRRSRDPAYELLITGGTYA
          CACIVLCRRSRDPAYELLITGGTYA
Retrocopy CACIVLCRRSRDPAYELLITGGTYA

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	0.34 RPM	152.04 RPM
SRP017611_brain	1.91 RPM	105.51 RPM
SRP017611_kidney	1.65 RPM	124.41 RPM
SRP017611_liver	0.07 RPM	23.71 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_1391 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_1391 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_1391 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 11 parental genes, and 19 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000009727	1 retrocopy	retro_amel_1275,
Bos taurus	ENSBTAG00000002415	2 retrocopies	retro_btau_1089, retro_btau_1650,
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,
Choloepus hoffmanni	ENSCHOG00000003785	2 retrocopies	retro_chof_162, retro_chof_1682,
Dasypus novemcinctus	ENSDNOG00000005619	3 retrocopies	retro_dnov_1371, retro_dnov_1520, retro_dnov_1616,
Echinops telfairi	ENSETEG00000010916	1 retrocopy	retro_etel_872,
Felis catus	ENSFCAG00000025746	1 retrocopy	retro_fcat_1860,
Mustela putorius furo	ENSMPUG00000017332	2 retrocopies	retro_mputfur_1641, retro_mputfur_1651,
Pteropus vampyrus	ENSPVAG00000004662	1 retrocopy	retro_pvam_394,
Ictidomys tridecemlineatus	ENSSTOG00000005615	1 retrocopy	retro_itri_1268,