RetrogeneDB ID: retro_cfam_260

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 1:48492879..48493983(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: ACTB
• Ensembl ID: ENSCAFG00000016020
• Aliases: ACTB, ACTA1
• Description: Canis lupus familiaris actin, beta (ACTB), mRNA. [Source:RefSeq mRNA;Acc:NM_001195845]

Sequence

>retro_cfam_260
GAAGAGGAGATCGCCGCTCTCGACAGTGGCTCTGCATGTGCAGGGCGGGCTTCGCCGGGGATGGCGCCCCCGAGCTGTGT
TCCCATCCATCATCGGGCGACCCCAGCCCTAGGGCATGATGGTGAGCATGGGCCAGAAGGACTCTTACGTGGGTGATGAG
GCCCTGACCAAGCAGGGCATCCTGACCCTCAGGTACCCCATCGAGCATGACATCGTCACCAACTGGGATGACGTGGAAAA
GACCTGGCACCACACCTTCTACAATGAGCTGCACGTGGCCTCTGAGGAGCACCCCGTGCTGCTGACCGAAGCCCCCCCGA
ACCCCAAGGCCAACCATGAGAAGATGACTCAGATCATGTTCGAGACGTTCAACACCTCAGCCATGTACGTGGCCATCTAG
GCTGTGCTCTCCCTGTACGCCTCTGGCCGCACCACTGGTATCGTCATGGACTCTGGGGATGGCATCACCCACACTGCCCA
TCGACGAGGGGTACGCCTCGCCCCACGCCGTCCTGCGTCTGGACCTGGCTGGCCGCGGCCTGGCCCACCACCTCATGACA
ATCCTCACCGAGCGTGGCTACAGCTTCACCACCGCTGCCGAGCAGGAGATCGTGCGTGACATTAAGGAGAAGCTCTGCTG
CGTTGCCCTGGACTTCGAGCAGGAGGTGGCCACGGCTGCGTCCTCGTCCTCCCTGGAGAAGAGCTAGGAGCTGCCCGAGG
GGCAGGTGATCACCGTCCAGCGGTTCTGCTGCCCAGAGGTGCTCTTCCAGCTTCCTTCCCGGGTGTGGAGTCCTGCGGCA
TCCACGAGACCACCTTCAACTCCATCGTGAAGTGTGATGTGGCAATCTGGGAGGACCTTTATGCCAACACGGTGCTGTCT
GGTGGAACCACCATGTACCCCGGCATCGCCGATGGGATGCAGAAGGGGATCACAGCCCTGGCCCCCAGCACGATGAAGAT
CAAGATTATTGCTCCTCCCAAACGCAAGTACTCCGCGTGGATCGGAGGCTCCAGGCTGGCCTCGCTGTCCACCTTCCAGC
AGGTGTGGCTCAGAAGCAGGAGTATGATGAGTCGGGCCCCTCCATCGTCCACTGCAAATGCTTC

Alignment

ORF - retro_cfam_260 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 80.0 %
• Parental protein coverage: 99.73 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 6

Retrocopy - Parental Gene Alignment:

Parental  DDDIAALVVDNGSG-MCKAGFAGDDAP-RAVFPSIVGRPRHQGVMVGMGQKDSYVGDEAQSKRGILTLKY
          ...IAAL..D.GS..MC.AGFAGD.AP.RAVFPSI.GRP...G.MV.MGQKDSYVGDEA..K.GILTL.Y
Retrocopy EEEIAAL--DSGSA<MCRAGFAGDGAP<RAVFPSIIGRPQP*GMMVSMGQKDSYVGDEALTKQGILTLRY

Parental  PIEHGIVTNWDDMEKIWHHTFYNELRVAPEEHPVLLTEAPLNPKANREKMTQIMFETFNTPAMYVAIQAV
          PIEH.IVTNWDD.EK.WHHTFYNEL.VA.EEHPVLLTEAP.NPKAN.EKMTQIMFETFNT.AMYVAI.AV
Retrocopy PIEHDIVTNWDDVEKTWHHTFYNELHVASEEHPVLLTEAPPNPKANHEKMTQIMFETFNTSAMYVAI*AV

Parental  LSLYASGRTTGIVMDSGDGVTHTV-PIYEGYALP-HAILRLDLAGRDLTDYLMKILTERGYSFTTTAERE
          LSLYASGRTTGIVMDSGDG.THT..P...G...P.HA.LRLDLAGR.L...LM.ILTERGYSFTT.AE.E
Retrocopy LSLYASGRTTGIVMDSGDGITHTA<PSTRGTPRP<HAVLRLDLAGRGLAHHLMTILTERGYSFTTAAEQE

Parental  IVRDIKEKLCYVALDFEQEMATAASSSSLEKSYELPDGQVITIGNERFRCPEALFQ-PSFLGMESCGIHE
          IVRDIKEKLC.VALDFEQE.ATAASSSSLEKS.ELP.GQVIT....RF.CPE.LFQ..SF.G.ESCGIHE
Retrocopy IVRDIKEKLCCVALDFEQEVATAASSSSLEKS*ELPEGQVITV--QRFCCPEVLFQ<ASFPGVESCGIHE

Parental  TTFNSIMKCDVDIRKDLYANTVLSGGTTMYPGIADRMQKEITALAPSTMKIKIIAPPERKYSVWIGGSIL
          TTFNSI.KCDV.I..DLYANTVLSGGTTMYPGIAD.MQK.ITALAPSTMKIKIIAPP.RKYS.WIGGS.L
Retrocopy TTFNSIVKCDVAIWEDLYANTVLSGGTTMYPGIADGMQKGITALAPSTMKIKIIAPPKRKYSAWIGGSRL

Parental  ASLSTFQQMWI-SKQEYDESGPSIVHRKCF
          ASLSTFQQ.W...KQEYDESGPSIVH.KCF
Retrocopy ASLSTFQQVWL<QKQEYDESGPSIVHCKCF

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	0.21 RPM	694.45 RPM
SRP017611_brain	0.95 RPM	361.16 RPM
SRP017611_kidney	0.00 RPM	277.03 RPM
SRP017611_liver	0.00 RPM	263.37 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_260 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_260 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_260 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 13 parental genes, and 44 retrocopies.

Species	Parental gene accession	Retrocopies number
Anas platyrhynchos	ENSAPLG00000010147	1 retrocopy	retro_apla_2,
Canis familiaris	ENSCAFG00000016020	3 retrocopies	retro_cfam_120, retro_cfam_260 , retro_cfam_934,
Callithrix jacchus	ENSCJAG00000000008	2 retrocopies	retro_cjac_243, retro_cjac_56,
Dipodomys ordii	ENSDORG00000010079	1 retrocopy	retro_dord_11,
Equus caballus	ENSECAG00000015935	2 retrocopies	retro_ecab_271, retro_ecab_994,
Felis catus	ENSFCAG00000006788	1 retrocopy	retro_fcat_1613,
Loxodonta africana	ENSLAFG00000009167	1 retrocopy	retro_lafr_116,
Macaca mulatta	ENSMMUG00000011153	1 retrocopy	retro_mmul_135,
Otolemur garnettii	ENSOGAG00000008348	1 retrocopy	retro_ogar_2637,
Petromyzon marinus	ENSPMAG00000004161	1 retrocopy	retro_pmar_4,
Pan troglodytes	ENSPTRG00000018890	27 retrocopies	retro_ptro_1042, retro_ptro_1051, retro_ptro_1076, retro_ptro_1143, retro_ptro_1272, retro_ptro_1515, retro_ptro_1756, retro_ptro_178, retro_ptro_2122, retro_ptro_2173, retro_ptro_2349, retro_ptro_2454, retro_ptro_263, retro_ptro_2805, retro_ptro_2854, retro_ptro_314, retro_ptro_3207, retro_ptro_3219, retro_ptro_3282, retro_ptro_3287, retro_ptro_3292, retro_ptro_3302, retro_ptro_3307, retro_ptro_387, retro_ptro_432, retro_ptro_53, retro_ptro_584,
Ictidomys tridecemlineatus	ENSSTOG00000006868	2 retrocopies	retro_itri_1675, retro_itri_531,
Xenopus tropicalis	ENSXETG00000025116	1 retrocopy	retro_xtro_6,