RetrogeneDB ID: retro_cfam_961

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 20:32865753..32866277(+)
• Located in intron of: ENSCAFG00000029086

Retrocopy information

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

Parental gene information

• Parental gene symbol: CENPH
• Ensembl ID: ENSCAFG00000007717
• Aliases: None
• Description: centromere protein H [Source:HGNC Symbol;Acc:17268]

Sequence

>retro_cfam_961
CAACCCAAATAGCAAGCAGTCATCAAGCCCTCCAACTCTGGAGTGGGAGGCAGGGAAGGTGGGCCAGCACAGGTCGCTGG
TGCCCAGGTGGTACATCCCGCGGACCTCTTGACCCTGCCACTCAGACTGAGAGCACAGACAAAACAGTAACTCTTGGAAT
ATAAATCAGTGGTTGATTACAAATGAAAAAACTCCAGAACAAATCATGCAAAATAAGTGAATTGAAGCTAAAATTGAAGA
CCTGGAAAATGAAGTTGGAAGAGTTGAAAATTGCTTTTGAAATGAAGGTTTCATTAGAGAGGATGCAACTTTCAACTGCA
CTTCAAAAAAACTAGAGTAAATTAACCCCAAGTGTGATCATGGATAACATGAAACATGTTATTAAAGCTAAATTAATAAT
GAAATCACACCAGGAGTCTTGGGATTTGAAGGAAAAACTGCTTGATGATGGAAAGATGAGATTACAAATAAGACAAACTT
TAGAATGTAAGGTTTTAGAAATACAGACTGAAAAGAGCAAACAG

Alignment

ORF - retro_cfam_961 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 65.76 %
• Parental protein coverage: 77.45 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  RPGEQAAGEPADCGAGGGEGGDDEPPQGAGAQAARPEARLTLLLRLRAQTKQQLLEYKSMVD-ANEEKTP
          .P..QA...P...G.GG.EGG...P.Q.AGAQ...P...LTL.LRLRAQTKQ.LLEYKS.VD..NE.KTP
Retrocopy QPK*QAVIKPSNSGVGGREGG---PAQVAGAQVVHPADLLTLPLRLRAQTKQ*LLEYKSVVD>TNE-KTP

Parental  EQLIQDKHIEAKIEDLEKEV-EEVKTAFEMKKLALDRMQLSIALQKNLEKIDPKTSVLMDNMKHVLKLNK
          EQ..Q.K.IEAKIEDLE.EV.EE.K.AFEM.K..L.RMQLS.ALQKN..K..P..SV.MDNMKHV.K..K
Retrocopy EQIMQNK*IEAKIEDLENEV>EELKIAFEM-KVSLERMQLSTALQKN*SKLTP--SVIMDNMKHVIKA-K

Parental  LIMKSHQESWDLEEKLLDVRKKRLELKQSSENKLLEIQTEKNKQ
          LIMKSHQESWDL.EKLLD..K.RL...Q..E.K.LEIQTEK.KQ
Retrocopy LIMKSHQESWDLKEKLLDDGKMRLQIRQTLECKVLEIQTEKSKQ

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	0.25 RPM	6.72 RPM
SRP017611_brain	0.08 RPM	0.87 RPM
SRP017611_kidney	0.26 RPM	3.83 RPM
SRP017611_liver	0.44 RPM	0.44 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_961 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_961 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_961 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 7 parental genes, and 12 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000007717	1 retrocopy	retro_cfam_961 ,
Choloepus hoffmanni	ENSCHOG00000011338	2 retrocopies	retro_chof_1939, retro_chof_982,
Monodelphis domestica	ENSMODG00000025601	1 retrocopy	retro_mdom_1859,
Mustela putorius furo	ENSMPUG00000014646	1 retrocopy	retro_mputfur_240,
Sarcophilus harrisii	ENSSHAG00000007822	4 retrocopies	retro_shar_805, retro_shar_806, retro_shar_807, retro_shar_809,
Tupaia belangeri	ENSTBEG00000011867	2 retrocopies	retro_tbel_4318, retro_tbel_4535,
Tarsius syrichta	ENSTSYG00000002098	1 retrocopy	retro_tsyr_199,