RetrogeneDB ID: retro_ecab_364

Retrocopy location

• Organism: Horse (Equus caballus)
• Coordinates: 16:55197629..55198028(+)
• Located in intron of: ENSECAG00000019984

Retrocopy information

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

Parental gene information

• Parental gene symbol: FAM96A
• Ensembl ID: ENSECAG00000010303
• Aliases: None
• Description: MIP18 family protein FAM96A [Source:RefSeq peptide;Acc:NP_001092912]

Sequence

>retro_ecab_364
GCTGCCTGGAAGCCCCGGATCATGGAGGAGGAGGGCTAGGGGATTACAAATTGAGTCAGACTCTGGAACCCAAAGAAGCC
TAAAACTTTGGAAGAATTGGAAGTGATAATGGAAAGTAAAGTAGAAGTTCAGGAACTAAATGAAGAAGACTGTCTGGTTA
TTATCAGGTTCACAGCACAATATTTTATTGCTATTTGGCGACTCTTATTGGGCTGTGCTTAAGAGTAAAACTTAAGTGGA
GTTTATCTTTGAAACCTACAATGGAAATCTACATTTCGGAAGGAGCCCACTCAAAATAAGAAGACGTCAATAGGCAGATA
AATGACAAAGTGAGTGGCAGGTGTGCAATGGAGACCCCCAACTTACTGGAAATGTGGGAACAAGTGGGTCCTTCAACCT

Alignment

ORF - retro_ecab_364 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 59.56 %
• Parental protein coverage: 83.75 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  AARQPRTMEEKALEVYDLIRTIRDPEKPNTLEELGVVTESCVEVQEINEEDYLVIIRFTP-TVPHCSLAT
          AA..PR.MEE.........R....P.KP.TLEEL.V..ES.VEVQE.NEED.LVIIRFT..T...C.LAT
Retrocopy AAWKPRIMEEEG*GITN*VR-LWNPKKPKTLEELEVIMESKVEVQELNEEDCLVIIRFTA<TIFYCYLAT

Parental  LIGLCLRVKLQRCLPFKHKLEIYISEGTHSTEEDINKQINDKERVAAAMENPNLREIVEQC-VLEP
          LIGLCLRVKL...L..K...EIYISEG.HS..ED.N.QINDK.....AME.PNL.E..EQ..VL.P
Retrocopy LIGLCLRVKLKWSLSLKPTMEIYISEGAHSK*EDVNRQINDKVSGRCAMETPNLLEMWEQV>VLQP

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	0.94 RPM
SRP021940_cerebellum	0.00 RPM	4.26 RPM
SRP021940_embryo	0.03 RPM	6.06 RPM
SRP021940_placental_villous	0.00 RPM	7.07 RPM
SRP021940_synovial_membrane	0.00 RPM	3.51 RPM
SRP021940_testis	0.06 RPM	10.81 RPM

ChIP-Seq

Equus caballus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ecab_364 retrocopy.

TSS

Equus caballus was not studied using FANTOM5 data.

Lab

retro_ecab_364 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ecab_364 has 4 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_2763
Pan troglodytes	retro_ptro_1870
Gorilla gorilla	retro_ggor_1921
Bos taurus	retro_btau_984

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Parental genes homology:

Parental genes homology involve 21 parental genes, and 37 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000002448	1 retrocopy	retro_amel_1707,
Bos taurus	ENSBTAG00000002012	2 retrocopies	retro_btau_509, retro_btau_984,
Canis familiaris	ENSCAFG00000017035	2 retrocopies	retro_cfam_1450, retro_cfam_439,
Callithrix jacchus	ENSCJAG00000004834	1 retrocopy	retro_cjac_1751,
Equus caballus	ENSECAG00000010303	1 retrocopy	retro_ecab_364 ,
Erinaceus europaeus	ENSEEUG00000000854	1 retrocopy	retro_eeur_323,
Felis catus	ENSFCAG00000004178	1 retrocopy	retro_fcat_1379,
Homo sapiens	ENSG00000166797	2 retrocopies	retro_hsap_2763, retro_hsap_522,
Gorilla gorilla	ENSGGOG00000016550	2 retrocopies	retro_ggor_1921, retro_ggor_481,
Loxodonta africana	ENSLAFG00000011114	1 retrocopy	retro_lafr_758,
Macropus eugenii	ENSMEUG00000005979	2 retrocopies	retro_meug_471, retro_meug_85,
Microcebus murinus	ENSMICG00000011072	1 retrocopy	retro_mmur_233,
Myotis lucifugus	ENSMLUG00000028233	2 retrocopies	retro_mluc_578, retro_mluc_893,
Mustela putorius furo	ENSMPUG00000000605	1 retrocopy	retro_mputfur_722,
Mus musculus	ENSMUSG00000032381	1 retrocopy	retro_mmus_1919,
Nomascus leucogenys	ENSNLEG00000026932	3 retrocopies	retro_nleu_156, retro_nleu_2577, retro_nleu_667,
Ochotona princeps	ENSOPRG00000015229	5 retrocopies	retro_opri_476, retro_opri_522, retro_opri_828, retro_opri_84, retro_opri_999,
Pongo abelii	ENSPPYG00000006544	1 retrocopy	retro_pabe_224,
Pan troglodytes	ENSPTRG00000007153	2 retrocopies	retro_ptro_1870, retro_ptro_390,
Sorex araneus	ENSSARG00000002068	3 retrocopies	retro_sara_54, retro_sara_597, retro_sara_742,
Tarsius syrichta	ENSTSYG00000004186	2 retrocopies	retro_tsyr_195, retro_tsyr_62,