RetrogeneDB ID: retro_cfam_1685

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 4:20175203..20175989(-)
• Located in intron of: ENSCAFG00000013808

Retrocopy information

• Ensembl ID: None
• Aliases: None
• Status: NOVEL

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_1685
ATAAACGCTACTCCAAACTTTAAGAAGCTTCATGAGGCTCGTTTTAAGGAAATGGAGTCCACTGATATATATTGAGAGGA
AAAAGAAACATTTTGAAGAACGCAACTCATTTAATGAACTGAGGAAGCAGCCGGTCACCAAAGAAGTGGTGGGGACTCCA
GTTCCTCTCCGGGGAAGGCTCCCTGAGGCTCGAACTCCCTCTGGCCAGTGACGCTCGCAGGGCCAGCCCCTGGGCCCTGC
AGGCCAGAGCACCTTGTGTGGGAAGGGGTCCGCCAAGCGGTCCATTCTATCGGCTACTAAAATGAATGTCAGGTTTTCAG
CTGCTACCAGAGATAATGAACTTAAGTGTTCACTGACCAAGACTCCAGCCAGAAAGTCTCCACATGTGACCGCACGTGGG
AGTACTCTAAAAGGCCAGGCTGTGCTTGGACATGCAAGTTAAAGACCGCGAAGGGGAATTCTGCTTCTGTTGTTAACCCA
TTTAAGTCAACAACTGAGGCAACACGGACTCCAGTCTCCGACAAGAAATCTGTGTTTGATCTCAAAGCAAGTCTGTCTCG
TCCCCTCAACTATGAGCCACACAAAGGCAAACTGAAACCATGGGGTCAACCTAAAGAAAATAATGCTCTCAAGCAACATG
TCAACAGAGTTAGCTTTCACAAGAAAACTTATAAACAACCTCCTCTCCAGACTCGGGAGGAACAACAGAAGCAACATGAA
CAAAGACGAAAGGAGAAGAAAGCAAAGGTTTTGGGAGCTCGAAGAGGCCTCATTATGGCTGAAGAT

Alignment

ORF - retro_cfam_1685 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.66 %
• Parental protein coverage: 60.18 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  ISATPNFKKLHEARFKEMESIDQYIE-RKKKHFEEHNSFNELKKQPVTKEVVVTPVPLRGRLPEARTPSS
          I.ATPNFKKLHEARFKEMES.D.Y.E..KK...E....FNEL.KQPVTKEVV.TPVPLRGRLPEARTPS.
Retrocopy INATPNFKKLHEARFKEMESTDIY*E>KKKHFEERNS-FNELRKQPVTKEVVGTPVPLRGRLPEARTPSG

Parental  QRHSQGQPLGPTGQSTLCGKGSAKRSILSATKMNVRFSAATKDNEHKRSLTKTPARKSPHVTVCGSTPKG
          Q..SQGQPLGP.GQSTLCGKGSAKRSILSATKMNVRFSAAT.DNE.K.SLTKTPARKSPHVT..GST.KG
Retrocopy Q*RSQGQPLGPAGQSTLCGKGSAKRSILSATKMNVRFSAATRDNELKCSLTKTPARKSPHVTARGSTLKG

Parental  QAVLG-TCKLKTAKGNSASVVTPFKLTTETAQTPVSNKKPVFDLKASLSRPLNYEPHKGKLKPWGQPKEN
          QAVLG.TCKLKTAKGNSASVV.PFK.TTE...TPVS.KK.VFDLKASLSRPLNYEPHKGKLKPWGQPKEN
Retrocopy QAVLG<TCKLKTAKGNSASVVNPFKSTTEATRTPVSDKKSVFDLKASLSRPLNYEPHKGKLKPWGQPKEN

Parental  SSVKQHANRVSFHKKTYKQPPLQTREEQRKQHEQRRKEKKAKVLGARRGLIMAED
          ...KQH.NRVSFHKKTYKQPPLQTREEQ.KQHEQRRKEKKAKVLGARRGLIMAED
Retrocopy NALKQHVNRVSFHKKTYKQPPLQTREEQQKQHEQRRKEKKAKVLGARRGLIMAED

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	0.04 RPM	9.53 RPM
SRP017611_brain	0.08 RPM	2.06 RPM
SRP017611_kidney	0.00 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_1685 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_1685 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_1685 has 0 orthologous retrocopies within eutheria group .

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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,