RetrogeneDB ID: retro_cfam_1568

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 35:16492293..16493130(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCAFG00000010021
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: ARPC1B
• Ensembl ID: ENSCAFG00000015081
• Aliases: None
• Description: actin related protein 2/3 complex, subunit 1B, 41kDa [Source:HGNC Symbol;Acc:704]

Sequence

>retro_cfam_1568
ACAGGTCGCAATGCCTACGTATGGACGCTGAAGGGCTGCACATGGAAGCCCACACTAGTCATCCTGCGGATCAACCGGGC
TGCCTGCTGTGTGCGCTGGGCCCCCCATGAGAACAAGTTTGCTGTGGGTAGTGGCTCCCGTGTCATCTCCATCTGCTATT
TTGAGCAGGAAAATGACTGGTGGGTGTGCAAGCGCATCAAGAAGCCCATTTGCTCCACGGTCCTCAGCCTGGACTGGCAC
CCCAACAATGTGCTCTTGGCAGGGGCTCCTGCGACTTCAAGTGCAGGATCTTCTCGGCCTACATCAAGGAGGTGGAGGAG
CGGCCAGCACCCACCCCGTGGGGCTCCAAGATGCCCTTTGGGGAGCTGATGTTTGAGTCTAGCAGTAGCTGTGGCTGGGT
GCACGGCACCTCTTTCCAGCCAGTGGCAGCCGCGTGGCCTGGGTCAGCCACGACAGCACCCTGTGCCTAGCCGATGCCGA
CAAGAAAATAGCTGTTGCCACTCTGGCCTCTGAAACGCTGCCACTGCTGGCCCTGACCTTCATCACAGAAAACAGTCTGG
TGGCAGCGGGCCACGACTGTTTTCCGGCGCTGTTTACCTATGACAGCACCACAGGGACACTGAGTTCTGGTGGGCGGCTG
GACGTGCCCAAGCAAAGCTCGCAGCGTGGCCTGACCGCCCGAAAGCGCTTCCAGAATCTGGACAAGAAGGCGAGCTCAGA
GGGCAGCGTGGCTCCTGGCTCCGGCCTGGACTCAGTGCATAAGAACAGCGTGAGCCAGATCTCGGGCTCAGCGGGGGCAA
GGCTGAGTGCTCACAGTTCTGCACCACAGGAATGGAT

Alignment

ORF - retro_cfam_1568 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 93.29 %
• Parental protein coverage: 75.27 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  TDRNAYVWTLKGRTWKPTLVILRINRAARCVRWAPHENKFAVGSGSRVISICYFEQENDWWVCKHIKKPI
          T.RNAYVWTLKG.TWKPTLVILRINRAA.CVRWAPHENKFAVGSGSRVISICYFEQENDWWVCK.IKKPI
Retrocopy TGRNAYVWTLKGCTWKPTLVILRINRAACCVRWAPHENKFAVGSGSRVISICYFEQENDWWVCKRIKKPI

Parental  RSTVLSLDWHPNNVLLAA-GSCDFKCRIFSAYIKEVEERPAPTPWGSKMPFGELMFESSSSCGWVHGVCF
          .STVLSLDWHPNNVLLA..GSCDFKCRIFSAYIKEVEERPAPTPWGSKMPFGELMFESSSSCGWVHG..F
Retrocopy CSTVLSLDWHPNNVLLAG<GSCDFKCRIFSAYIKEVEERPAPTPWGSKMPFGELMFESSSSCGWVHGTSF

Parental  S-ASGSRVAWVSHDSTMCLADADKKMAVATLASETLPLLALTFITENSLVAAGHDCFPVLFTYDSTTGTL
          ..ASGSRVAWVSHDST.CLADADKK.AVATLASETLPLLALTFITENSLVAAGHDCFP.LFTYDSTTGTL
Retrocopy Q<ASGSRVAWVSHDSTLCLADADKKIAVATLASETLPLLALTFITENSLVAAGHDCFPALFTYDSTTGTL

Parental  SSGGRLDVPKQSSQRGLTARERFQNLDKKASSEGSVASGSGLDSLHKNSVSQIS-VLSGGKAECSQFCTT
          SSGGRLDVPKQSSQRGLTAR.RFQNLDKKASSEGSVA.GSGLDS.HKNSVSQIS..LSGGKAECSQFCTT
Retrocopy SSGGRLDVPKQSSQRGLTARKRFQNLDKKASSEGSVAPGSGLDSVHKNSVSQIS<GLSGGKAECSQFCTT

Parental  GMD
          GMD
Retrocopy GMD

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	60.69 RPM
SRP017611_brain	0.00 RPM	11.99 RPM
SRP017611_kidney	1.06 RPM	631.98 RPM
SRP017611_liver	0.00 RPM	16.82 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_1568 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_1568 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_1568 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 12 parental genes, and 18 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000046248	2 retrocopies	retro_btau_1547, retro_btau_473,
Canis familiaris	ENSCAFG00000015081	1 retrocopy	retro_cfam_1568 ,
Callithrix jacchus	ENSCJAG00000015849	1 retrocopy	retro_cjac_2365,
Echinops telfairi	ENSETEG00000009924	2 retrocopies	retro_etel_1076, retro_etel_1275,
Gorilla gorilla	ENSGGOG00000013186	2 retrocopies	retro_ggor_1337, retro_ggor_1455,
Microcebus murinus	ENSMICG00000017424	1 retrocopy	retro_mmur_602,
Myotis lucifugus	ENSMLUG00000010933	1 retrocopy	retro_mluc_974,
Mustela putorius furo	ENSMPUG00000016522	1 retrocopy	retro_mputfur_1578,
Mus musculus	ENSMUSG00000029622	2 retrocopies	retro_mmus_1340, retro_mmus_3623,
Otolemur garnettii	ENSOGAG00000010872	2 retrocopies	retro_ogar_2380, retro_ogar_3087,
Rattus norvegicus	ENSRNOG00000000991	2 retrocopies	retro_rnor_1105, retro_rnor_967,
Sus scrofa	ENSSSCG00000007625	1 retrocopy	retro_sscr_374,