RetrogeneDB ID: retro_ecab_447

Retrocopy location

• Organism: Horse (Equus caballus)
• Coordinates: 18:46544488..46545646(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSECAG00000015297
• Aliases: None
• Description: None

Sequence

>retro_ecab_447
GTGATAAAGTATCACTTTCAACACTGGGAATTTTCATTAACATTGACAGATGATATTTACAGTTGCTACCAATCCTTCAA
CAACCAGAGTGATTCGGAAAAGGAGATGCAGAAAATGAATCCACACAAGATTGATATAAGCGCAGTATATTCCCACAGGC
TCAATCAACACAATACAGTGAAGCTGGGAACTTTCCAGGCTCAGGAAAAAGAATTAGTGTTTGACATGGACATGACAGAC
TAGACGATGTGAGGAGATGTTGTAGTTCTGCAGGCATATATTCTGAGTGCTGGACCCTCATGAAGATGGCCATAATTATC
ATCCACCAGACATTGACAGAGGACAGGAGATTTAAGCGTCATCTCTGGGTATATTCTAGAAGGAGAGGCGTTCATCGTTG
AGTCTGTGATGAATCAGTTAGAAAATTGTTCCCAGTACGTTCTGGGATAGATGAGTATTTGAGTCTTGTAAAGGGTGGTC
AAGAGGTCAAAAAGACAGTTTGTCTAAGTGAAAAAATTTACCCTTTTGTTAGGAAATATAAACATAATAAAAGACTGCTT
TGAAGAATATGCCTTGGTTGATCAAGATATTCTTGAAAATAAAGAAAGATGGGATAGGATGTTAGCCCTTCTTCCTAGAG
TAATTCATGATTGCTTCCAAAAACTTCAACAAGGCTTCCAAAAGCATTACAATCCACTTCAGGATTGGCAGCATTTGAAG
AGGGTAGCCAGCAGATGTGAGAATAACATCAAAAAAGACAAATGTCGATCCTGGCTTGAGTGGGAGATCATGCTCTGGTA
CTGTTTTCCACAGCTGGATATTAATGTTAGCAAAGGAATCAGTCATTTACTGAAAAGTCCTTTTAGTGTTCGTCCTAAAA
CAGGTTGCATTTTTGTGCCTATTGATTTACAGAGAGTAGATCGATTTGATCCATTTACTGTTCCAGCCATAGGTTCCATC
TACCATGAAGTGGATAGCATTTCCACTAATGAAGAGAAAAAAGAGGAGAACGAAGTTGAATCTGATATCAAACATAGAAT
CAGAGACTATAAGAAGACCAATCTAACTCCTTATGTAAAAGCTTTTGAACAGTTTCTTGAAAACCTGGATAAATCCCAAA
AAAAGGAGTTCTCAAGAAGTGATTTACAAAACGATTTC

Alignment

ORF - retro_ecab_447 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 70.81 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  VVKNYFQHREFSFTLKDDIYIRYQSFNNQSDLEKEMQKMNPYKIDIGAVYSHRPNQHNTVKLGAFQAQEK
          V.K..FQH.EFS.TL.DDIY..YQSFNNQSD.EKEMQKMNP.KIDI.AVYSHR.NQHNTVKLG.FQAQEK
Retrocopy VIKYHFQHWEFSLTLTDDIYSCYQSFNNQSDSEKEMQKMNPHKIDISAVYSHRLNQHNTVKLGTFQAQEK

Parental  ELVFDIDMTD-YDDVRRCCSSADICSKCWTLMTMAIRIIDRALKGKDFGFKHRLWVYSGRRGVHCWVCDE
          ELVFD.DMTD..DDVRRCCSSA.I.S.CWTLM.MAI.II...L...D..FK..LWVYS.RRGVH..VCDE
Retrocopy ELVFDMDMTD<LDDVRRCCSSAGIYSECWTLMKMAIIIIHQTLT-EDRRFKRHLWVYSRRRGVHR*VCDE

Parental  SVRKLSSAVRSGIVEYLSLVKGGQDVKKKVHLSENVH-PF-VRKSISIIKKYFEGYALVGQDILENKESW
          SVRKL...VRSGI.EYLSLVKGGQ.VKK.V.LSE....PF.....I.IIK..FE.YALV.QDILENKE.W
Retrocopy SVRKLFP-VRSGIDEYLSLVKGGQEVKKTVCLSEKIY<PF<LLGNINIIKDCFEEYALVDQDILENKERW

Parental  DKILALVYPSPMHN---DLQQNFQKHHSSLQRWEYLKKAASQCPSNIKNEKCGPWLEWEIMLQYCFPRLD
          D..LAL..P...H.....LQQ.FQKH...LQ.W..LK..AS.C..NIK..KC..WLEWEIML.YCFP.LD
Retrocopy DRMLALL-PRVIHDCFQKLQQGFQKHYNPLQDWQHLKRVASRCENNIKKDKCRSWLEWEIMLWYCFPQLD

Parental  INVSKGINHLLKSPFSVHPKTGRISVPIDLQKVDQFDPFAVPTISSICHELDAIFTSEAEKEENQAESDI
          INVSKGI.HLLKSPFSV.PKTG.I.VPIDLQ.VD.FDPF.VP.I.SI.HE.D.I.T.E..KEEN..ESDI
Retrocopy INVSKGISHLLKSPFSVRPKTGCIFVPIDLQRVDRFDPFTVPAIGSIYHEVDSISTNEEKKEENEVESDI

Parental  KHRTRDYKKTSLAPYVKVFEQFLENLDKSRKGELLKKSDLQKDF
          KHR.RDYKKT.L.PYVK.FEQFLENLDKS.K.E....SDLQ.DF
Retrocopy KHRIRDYKKTNLTPYVKAFEQFLENLDKSQKKE-FSRSDLQNDF

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
SRP021940_articular_cartilage	0.00 RPM	0.06 RPM
SRP021940_cerebellum	0.00 RPM	0.10 RPM
SRP021940_embryo	0.00 RPM	16.62 RPM
SRP021940_placental_villous	0.00 RPM	2.79 RPM
SRP021940_synovial_membrane	0.00 RPM	4.31 RPM
SRP021940_testis	0.00 RPM	16.50 RPM

ChIP-Seq

Equus caballus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ecab_447 retrocopy.

TSS

Equus caballus was not studied using FANTOM5 data.

Lab

retro_ecab_447 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ecab_447 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 12 parental genes, and 13 retrocopies.

Species	Parental gene accession	Retrocopies number
Equus caballus	ENSECAG00000015297	1 retrocopy	retro_ecab_447 ,
Homo sapiens	ENSG00000198056	1 retrocopy	retro_hsap_339,
Mustela putorius furo	ENSMPUG00000001603	1 retrocopy	retro_mputfur_587,
Nomascus leucogenys	ENSNLEG00000017443	1 retrocopy	retro_nleu_1780,
Oryctolagus cuniculus	ENSOCUG00000003458	1 retrocopy	retro_ocun_1265,
Procavia capensis	ENSPCAG00000007103	1 retrocopy	retro_pcap_174,
Pongo abelii	ENSPPYG00000004672	1 retrocopy	retro_pabe_356,
Pan troglodytes	ENSPTRG00000022987	1 retrocopy	retro_ptro_271,
Pteropus vampyrus	ENSPVAG00000008017	2 retrocopies	retro_pvam_153, retro_pvam_703,
Sus scrofa	ENSSSCG00000000408	1 retrocopy	retro_sscr_499,
Tupaia belangeri	ENSTBEG00000012998	1 retrocopy	retro_tbel_2255,
Tursiops truncatus	ENSTTRG00000002153	1 retrocopy	retro_ttru_352,