RetrogeneDB ID: retro_cfam_978

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 20:11150794..11151692(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: TUBA1C
• Ensembl ID: ENSCAFG00000008661
• Aliases: None
• Description: tubulin, alpha 1c [Source:HGNC Symbol;Acc:20768]

Sequence

>retro_cfam_978
TTCTCCTCTTCCTTTCTGCCATCTGCTTGACAACCAAAAAGCAGCACCACGAGTGAATGAATCTCCATACATGTTGGCCA
GTCTGGTGTTCATATTAACAATGCCTGCTGAGAGCTCTATTTCCTAGAACACAGCATCCAGCCCAATGGTCAGATGTCAG
GAGACAAGACTGTTGGGGAAGATAACTCTTTGAACACCTTCTTCGATGAGATAGGTGCTGGCAAGCATGTATGCAGGGCA
GTGTTTATAGACCTGGAACCACAGTCACTGATGAAGTTCACACTGGCACTTCCTGCCAGCTCTTCTACCCTTAGCAGCTT
ATCACAGGCAAGGAAGATGCTGCCAGTAACTACACTCAGGGGCACTACACCATTGGCAAGAAGGTCATTGGCCTTGTCTT
GGACCAAATTCAGAAACTGGCTGACCAGTGCATAGTTCTTCAGGGTTTCTTGGTTTTCCATAGCTTTGTAGGGACAGCTA
GTTCCAGATTCACCTCCCTGCTGAGGGAACATCTCTCTGTCTATTATAGTAAGAAGTCCAAGCTGGAGTTCTCCCATTTA
CCCAGCCCCTCTGGTTTCTACAGCTGTAGTTGACCCCTACAACTTCATCCTCACTACCCATACCACCCTAGAACACTCTA
ATTGTGTCTCCATGGTAGACAACAAGGCTATCTATGACATCTGTTGTAGAAACTTCGATATTAAACACATAGCCTACATT
AACCTGAATAGGTTGATAAGTCAGATTGTATTCTCCATAACTGCTTCTGATGGAGTTCTGAATGCTGATCTGACAATTAT
AGAACAACCTGGTGCCCTATCCTCCCATCCACTTCCCTCTGACTACATATGCTCCTGTCATCTCTGCTGAGAAAGCCTAC
CATGAACAGCTTTCACTG

Alignment

ORF - retro_cfam_978 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 69.48 %
• Parental protein coverage: 59.49 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  FNTGTTSKSREPGCVSERECISIHVGQAGVQIGNACWELYCLEHGIQPDGQMPSDKTIGGGDDSFNTFFS
          F..........P......E.ISIHVGQ.GV.I.NAC.ELY.LEH.IQP.GQM..DKT.G..D.S.NTFF.
Retrocopy FSSSFLPSA*QPKSSTTSE*ISIHVGQSGVHINNAC*ELYFLEHSIQPNGQMSGDKTVGE-DNSLNTFFD

Parental  ETGAGKHVPRAVFVDLEP-TVIDEVRTGTYRQLFHPEQLITGKEDAANNYARGHYTIGKEIIDLVLDRIR
          E.GAGKHV.RAVF.DLEP.TV.DEV.TGT..QLF.P.QLITGKEDAA.NY..GHYTIGK..I.LVLD.I.
Retrocopy EIGAGKHVCRAVFIDLEP<TVTDEVHTGTSCQLFYP*QLITGKEDAASNYTQGHYTIGKKVIGLVLDQIQ

Parental  KLADQCTGLQGFLVFHSFGGGTGSGFTSLLMERLSVDYGKKSKLEFS-IYPAPQVSTAVVEPYNSILTTH
          KLADQC..LQGFLVFHSF.G...S.FTSLL.E.LSV.Y.KKSKLEFS.IYPAP.VSTAVV.PYN.ILTTH
Retrocopy KLADQCIVLQGFLVFHSFVGTASSRFTSLLREHLSVYYSKKSKLEFS>IYPAPLVSTAVVDPYNFILTTH

Parental  TTLEHSDCAFMVDNEAIYDICRRNLDIERPTYTNLNRLISQIVSSITASLRFDGALNVDLT-EFQTNLVP
          TTLEHS.C..MVDN.AIYDIC.RN.DI....Y.NLNRLISQIV.SITAS...DG.LN.DLT....T...P
Retrocopy TTLEHSNCVSMVDNKAIYDICCRNFDIKHIAYINLNRLISQIVFSITAS---DGVLNADLT<NYRTTWCP

Parental  -YPRIHFPLATYAPVISAEKAYHEQLTV
          .YP.IHFPL.TYAPVISAEKAYHEQL..
Retrocopy <YPPIHFPLTTYAPVISAEKAYHEQLSL

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	45.95 RPM
SRP017611_brain	0.00 RPM	6.27 RPM
SRP017611_kidney	0.00 RPM	120.19 RPM
SRP017611_liver	0.00 RPM	19.00 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_978 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_978 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_978 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 12 parental genes, and 24 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000039992	1 retrocopy	retro_btau_840,
Canis familiaris	ENSCAFG00000005248	1 retrocopy	retro_cfam_1124,
Canis familiaris	ENSCAFG00000008640	8 retrocopies	retro_cfam_1481, retro_cfam_1751, retro_cfam_1895, retro_cfam_1917, retro_cfam_1979, retro_cfam_2000, retro_cfam_463, retro_cfam_926,
Canis familiaris	ENSCAFG00000008661	2 retrocopies	retro_cfam_960, retro_cfam_978 ,
Canis familiaris	ENSCAFG00000010412	1 retrocopy	retro_cfam_1418,
Choloepus hoffmanni	ENSCHOG00000008444	2 retrocopies	retro_chof_179, retro_chof_360,
Erinaceus europaeus	ENSEEUG00000004068	1 retrocopy	retro_eeur_669,
Felis catus	ENSFCAG00000024852	1 retrocopy	retro_fcat_361,
Felis catus	ENSFCAG00000028689	3 retrocopies	retro_fcat_1802, retro_fcat_254, retro_fcat_798,
Macropus eugenii	ENSMEUG00000010779	2 retrocopies	retro_meug_1648, retro_meug_2174,
Oryctolagus cuniculus	ENSOCUG00000028032	1 retrocopy	retro_ocun_111,
Otolemur garnettii	ENSOGAG00000009435	1 retrocopy	retro_ogar_240,