RetrogeneDB ID: retro_cfam_98

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 16:12956940..12958353(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCAFG00000003207
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCAFG00000017071
• Aliases: None
• Description: None

Sequence

>retro_cfam_98
ATGCAGAGCAATAAAACCTTTAACTTGGAGAAGCAAAACCATACTCCAAGGAAGCATCATCAGCATCACCACCAGCAGCA
CCACCAGCAGCAACAGCAGCAACCACCACCGCCACCAATACCTGCAAATGGGCAACAAGCCAGCAGCCAAAATGAAGACT
TGACTATTGACCTGAAGAGTTTTAGGAAACCAGGAGAGAAGACCTTCACCCAACGTAGCCGGCTCTTTGTGGGCAATCTT
CCTCCTGATATCACTGAAGAGGAGATGAGGAAACTATTTGAGAAATACGGGAAAGCAGGTGAAGTCTTCATTCATAAGGA
TAAGGGCTTTGGCTTTATCCGCTTGGAAACACGAACCTTAGCGGAGATTGCCAAAGTAGAATTGGACAACATGCCACTTC
GTGGAAAGCAGCTGCGTGTGCGTTTTGCCTGCCATAGTGCATCCCTTACAGTCCGAAACCTTCCTCAGTATGTTTCCAAT
GAACTGCTGGAGGAAGCCTTTTCCGTGTTTGGCCAGGTGGAGAGGGCTGTAGTCATCGTGGATGATCGAGGAAGGCCCTC
AGGAAAAGGCATTGTTGAATTCTCAGGGAAGCCAGCTGCTCGGAAAGCTCTGGACAGGTGCAGTGAAGGCTCTTTCCTGC
TAACCACATTTCCTAGGCCTGTGACTGTGGAGCCCATGGACCAGTTGGATGATGAAGAGGGACTTCCAGAGAAACTGGTT
ATAAAGAATCAGCAATTTCACAAGGAGCGAGAGCAGCCACCCAGATTTGCACAGCCTGGCTCCTCTGAGTATGAGTATGC
CATGCGCTGGAAGGCACTGATTGAGATGGAGAAGCAGCAGCAGGACCAAGTGGACCGCAACATCAAGGAAGCTCGTGAGA
AGCTGGAGATGGAGATGGAGGCTGCTCGCCATGAGCACCAGGTCATGCTAATGAGACAGGATTTGATGAGGCGTCAAGAA
GAACTTAGGAGGATGGAAGAGCTGCATAACCAAGAAGTGCAAAAACGAAAGCAACTGGAGCTCAGGCAAGAGGAGGAGCG
CAGGCGCCGAGAGGAAGAGATGCGGCGGCAACAGGAAGAAATGATGCGGCGACAGCAGGAAGGATTCAAGGGAACATTCC
CTGATGCGAGAGAACAGGAGATACGGATGGGGCAGATGGCTATGGGAGGTGCTATGGGCATAAACAATAGAGGTGCCATG
CCCCCTGCTCCAGTGCCAGCTGGTACCCCAGCTCCTCCAGAACCTGCCACTATGATGCCAGATGGAACCTTGGGATTGAC
CCCACCAACAACTGAATGCTTTGGCCAGGCTGCTACAATGGAAGGAATTGGGGCAATTGGTGGAACCCCTCCTGCATTCA
ACCGTGCAGCTCCTGGAGCTGAATTTGCTCCAAACAAACGTTGCCGATACTAA

Alignment

ORF - retro_cfam_98 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 98.72 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MQSNKTFNLEKQNHTPRKHHQHHHQQHHQQQQQQPPPPPIPANGQQASSQNEGLTIDLKNFRKPGEKTFT
          MQSNKTFNLEKQNHTPRKHHQHHHQQHHQQQQQQPPPPPIPANGQQASSQNE.LTIDLK.FRKPGEKTFT
Retrocopy MQSNKTFNLEKQNHTPRKHHQHHHQQHHQQQQQQPPPPPIPANGQQASSQNEDLTIDLKSFRKPGEKTFT

Parental  QRSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKDKGFGFIRLETRTLAEIAKVELDNMPLRGKQLRV
          QRSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKDKGFGFIRLETRTLAEIAKVELDNMPLRGKQLRV
Retrocopy QRSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKDKGFGFIRLETRTLAEIAKVELDNMPLRGKQLRV

Parental  RFACHSASLTVRNLPQYVSNELLEEAFSVFGQVERAVVIVDDRGRPSGKGIVEFSGKPAARKALDRCSEG
          RFACHSASLTVRNLPQYVSNELLEEAFSVFGQVERAVVIVDDRGRPSGKGIVEFSGKPAARKALDRCSEG
Retrocopy RFACHSASLTVRNLPQYVSNELLEEAFSVFGQVERAVVIVDDRGRPSGKGIVEFSGKPAARKALDRCSEG

Parental  SFLLTTFPRPVTVEPMDQLDDEEGLPEKLVIKNQQFHKEREQPPRFAQPGSFEYEYAMRWKALIEMEKQQ
          SFLLTTFPRPVTVEPMDQLDDEEGLPEKLVIKNQQFHKEREQPPRFAQPGS.EYEYAMRWKALIEMEKQQ
Retrocopy SFLLTTFPRPVTVEPMDQLDDEEGLPEKLVIKNQQFHKEREQPPRFAQPGSSEYEYAMRWKALIEMEKQQ

Parental  QDQVDRNIKEAREKLEMEMEAARHEHQVMLMRQDLMRRQEELRRMEELHNQEVQKRKQLELRQEEERRRR
          QDQVDRNIKEAREKLEMEMEAARHEHQVMLMRQDLMRRQEELRRMEELHNQEVQKRKQLELRQEEERRRR
Retrocopy QDQVDRNIKEAREKLEMEMEAARHEHQVMLMRQDLMRRQEELRRMEELHNQEVQKRKQLELRQEEERRRR

Parental  EEEMRRQQEEMMRRQQEGFKGTFPDAREQEIRMGQMAMGGAMGINNRGAMPPAPVPAGTPAPPGPATMMP
          EEEMRRQQEEMMRRQQEGFKGTFPDAREQEIRMGQMAMGGAMGINNRGAMPPAPVPAGTPAPP.PATMMP
Retrocopy EEEMRRQQEEMMRRQQEGFKGTFPDAREQEIRMGQMAMGGAMGINNRGAMPPAPVPAGTPAPPEPATMMP

Parental  DGTLGLTPPTTERFGQAATMEGIGAIGGTPPAFNRAAPGAEFAPNKRRRY
          DGTLGLTPPTTE.FGQAATMEGIGAIGGTPPAFNRAAPGAEFAPNKR.RY
Retrocopy DGTLGLTPPTTECFGQAATMEGIGAIGGTPPAFNRAAPGAEFAPNKRCRY

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	4.91 RPM	100.34 RPM
SRP017611_brain	1.11 RPM	32.71 RPM
SRP017611_kidney	2.05 RPM	61.94 RPM
SRP017611_liver	1.02 RPM	35.02 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_98 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_98 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_98 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 22 parental genes, and 32 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000016057	2 retrocopies	retro_amel_1438, retro_amel_795,
Bos taurus	ENSBTAG00000012152	2 retrocopies	retro_btau_1027, retro_btau_313,
Canis familiaris	ENSCAFG00000003595	1 retrocopy	retro_cfam_198,
Canis familiaris	ENSCAFG00000017071	1 retrocopy	retro_cfam_98 ,
Callithrix jacchus	ENSCJAG00000036744	1 retrocopy	retro_cjac_3990,
Equus caballus	ENSECAG00000008502	2 retrocopies	retro_ecab_357, retro_ecab_427,
Felis catus	ENSFCAG00000014807	2 retrocopies	retro_fcat_1219, retro_fcat_147,
Homo sapiens	ENSG00000147140	1 retrocopy	retro_hsap_1699,
Gorilla gorilla	ENSGGOG00000006194	1 retrocopy	retro_ggor_1273,
Microcebus murinus	ENSMICG00000000232	1 retrocopy	retro_mmur_569,
Myotis lucifugus	ENSMLUG00000002489	1 retrocopy	retro_mluc_622,
Mustela putorius furo	ENSMPUG00000004937	1 retrocopy	retro_mputfur_937,
Mus musculus	ENSMUSG00000031311	2 retrocopies	retro_mmus_3652, retro_mmus_632,
Nomascus leucogenys	ENSNLEG00000001278	1 retrocopy	retro_nleu_1344,
Oryctolagus cuniculus	ENSOCUG00000021848	2 retrocopies	retro_ocun_1317, retro_ocun_1804,
Otolemur garnettii	ENSOGAG00000004834	3 retrocopies	retro_ogar_1525, retro_ogar_546, retro_ogar_593,
Pongo abelii	ENSPPYG00000020451	1 retrocopy	retro_pabe_1398,
Pan troglodytes	ENSPTRG00000022010	1 retrocopy	retro_ptro_1150,
Pteropus vampyrus	ENSPVAG00000016503	1 retrocopy	retro_pvam_444,
Rattus norvegicus	ENSRNOG00000003689	2 retrocopies	retro_rnor_1178, retro_rnor_1503,
Sorex araneus	ENSSARG00000007959	2 retrocopies	retro_sara_661, retro_sara_663,
Drosophila melanogaster	FBgn0004227	1 retrocopy	retro_dmel_11,