RetrogeneDB ID: retro_cfam_578

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 13:49386201..49387076(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCAFG00000002332
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: NUSAP1
• Ensembl ID: ENSCAFG00000009538
• Aliases: None
• Description: nucleolar and spindle associated protein 1 [Source:HGNC Symbol;Acc:18538]

Sequence

>retro_cfam_578
GGTAATGAAGATTCAAAGGTACCTGCAGAAAGAAAGAAGGCTCTCTACGCAGATGGGTTTTCCAAACCTGGAAAAAGTAA
AAGAACTATAAGTGCTACTCCAAACTTTAAGAAGCTTCATGAGGCTCGTTTTAAGGAAATGGAGTCCATTGATCAATATA
TTGAAAGGAAAAAGAAACATTTTGAAGAACACAACTCATTTAATGAACTGAAGAAGCAGCCGGTCACCAAAGAAGTGGTG
GTGACTCCAGTTCCTCTCCGGGGAAGGCTCCCTGAGGCTCGAACTCCCTCCAGCCAGCGCCACTCACAGGGCCAGCCCCT
GGGCCCTACAGGCCAGAGCACCTTGTGTGGGAAGGGGTCTGCCAAGCGTTCCATTCTATCAGCAACTAAGATGAACGTCA
GGTTTTCAGCTGCTACCAAAGATAATGAACATAAGCATTCATTGACCAAGACTCCAGCCAGAAAGTCTCCACATGTGACC
ATATGTGGGAGTACCCCAAAAGGCCAGGCTGTGGTCAGGACATGCAAGTTAAAGACCGCAAAGGGGAATTCTGCTTCTGT
TGTTACCCATTCAAATTGACAACTGAGGCAGCACGGACTCCAGTCTCCAACAAGAAACCGGTATTTGATCTCAAAGCAAG
TCTGTCTCATCCCCTCAACTATGAACCACACAAAGGCAAACTGAAACCATGGGGTCAACCTAAAGAAAATAGTTCGCTCA
AGCAACATGCCAACAGAGTTAGCTTCCACAAGAAAACTTATAAACAACCTCCTCTCCAGACTCAGGAAGAACAACGGAAG
CAACATGAACAAAGACGAAAGGAGAAGAAAGCAAAGGTTTTGGGAGCTCGAAGAGGCCTCATTATGGCTGAAGAT

Alignment

ORF - retro_cfam_578 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 96.25 %
• Parental protein coverage: 66.82 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  GNEDSKVPAERKKHLYADGFSKPGKSKRTISATPNFKKLHEARFKEMESIDQYIERKKKHFEEHNSFNEL
          GNEDSKVPAERKK.LYADGFSKPGKSKRTISATPNFKKLHEARFKEMESIDQYIERKKKHFEEHNSFNEL
Retrocopy GNEDSKVPAERKKALYADGFSKPGKSKRTISATPNFKKLHEARFKEMESIDQYIERKKKHFEEHNSFNEL

Parental  KKQPVTKEVVVTPVPLRGRLPEARTPSSQRHSQGQPLGPTGQSTLCGKGSAKRSILSATKMNVRFSAATK
          KKQPVTKEVVVTPVPLRGRLPEARTPSSQRHSQGQPLGPTGQSTLCGKGSAKRSILSATKMNVRFSAATK
Retrocopy KKQPVTKEVVVTPVPLRGRLPEARTPSSQRHSQGQPLGPTGQSTLCGKGSAKRSILSATKMNVRFSAATK

Parental  DNEHKRSLTKTPARKSPHVTVCGSTPKGQAVLGTCKLKTAKGNSASVVT-PFKLTTETAQTPVSNKKPVF
          DNEHK.SLTKTPARKSPHVT.CGSTPKGQAV..TCKLKTAKGNSASVVT.PFKLTTE.A.TPVSNKKPVF
Retrocopy DNEHKHSLTKTPARKSPHVTICGSTPKGQAVVRTCKLKTAKGNSASVVT<PFKLTTEAARTPVSNKKPVF

Parental  DLKASLSRPLNYEPHKGKLKPWGQPKENSSVKQHANRVSFHKKTYKQPPLQTREEQRKQHEQRRKEKKAK
          DLKASLS.PLNYEPHKGKLKPWGQPKENSS.KQHANRVSFHKKTYKQPPLQT.EEQRKQHEQRRKEKKAK
Retrocopy DLKASLSHPLNYEPHKGKLKPWGQPKENSSLKQHANRVSFHKKTYKQPPLQTQEEQRKQHEQRRKEKKAK

Parental  VLGARRGLIMAED
          VLGARRGLIMAED
Retrocopy VLGARRGLIMAED

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	0.88 RPM	9.53 RPM
SRP017611_brain	0.00 RPM	2.06 RPM
SRP017611_kidney	0.07 RPM	2.84 RPM
SRP017611_liver	0.00 RPM	0.22 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_578 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_578 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_578 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

Parental genes homology involve 8 parental genes, and 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000010774	1 retrocopy	retro_btau_1714,
Canis familiaris	ENSCAFG00000009538	3 retrocopies	retro_cfam_1685, retro_cfam_2137, retro_cfam_578 ,
Cavia porcellus	ENSCPOG00000012875	1 retrocopy	retro_cpor_993,
Cavia porcellus	ENSCPOG00000020956	1 retrocopy	retro_cpor_258,
Myotis lucifugus	ENSMLUG00000009782	1 retrocopy	retro_mluc_389,
Mustela putorius furo	ENSMPUG00000008844	1 retrocopy	retro_mputfur_1626,
Otolemur garnettii	ENSOGAG00000034763	1 retrocopy	retro_ogar_3125,
Tupaia belangeri	ENSTBEG00000014283	1 retrocopy	retro_tbel_4088,