RetrogeneDB ID: retro_ecab_687

Retrocopy location

• Organism: Horse (Equus caballus)
• Coordinates: 28:23866205..23866561(+)
• Located in intron of: ENSECAG00000011449

Retrocopy information

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

Parental gene information

• Parental gene symbol: MRPL40
• Ensembl ID: ENSECAG00000009876
• Aliases: None
• Description: mitochondrial ribosomal protein L40 [Source:HGNC Symbol;Acc:14491]

Sequence

>retro_ecab_687
TCACAAATTAGAGACACCCACCAGCGAGCTTCATTGTTGACCTTCTGGAACTCATTCCCATGACAGCAGACCCTTTCTGC
GAAAGAAGGTAAATCCTAAAAAGACCAAGCAGGAAATGACCTTTTAACAAAGAGGATCCGACTACCGGGAAAACTAGCCA
AGAGATAATTCCCATCGAAGATTTTATTACTCCTGTGAGGTTCTTGAATAAAGCAAGACAGCGGCCTCAGGTGGAGTTCC
TTTTTGAAGAGGGTAAGAGGAGAGCTCTGCTTCTGAAAAAGTGGTTGCTGTACAAGCAGCGAAAGCATGAGATGGAGAGG
GACGCCATCAGGTCCGTGCTTGAGGCTCAGCAGGAA

Alignment

ORF - retro_ecab_687 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 69.6 %
• Parental protein coverage: 64.36 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  TQIRDTRRRASLLSFW-DLVPMRAE-PLRKKKKVDPK-KDQAVKDRLKKRIR-RLEKASQELIPIEDFIT
          .QIRDT..RASLL.FW..L.PM.A..P...KK.V.PK.KDQA..D.L.KRIR....K.SQE.IPIEDFIT
Retrocopy SQIRDTHQRASLLTFW<ELIPMTAD<PFLRKK-VNPK<KDQAGNDLLTKRIR<TTGKTSQEIIPIEDFIT

Parental  PVKFLDQARQRPHTELPFEEGERRALLLKKWSLYKQREHEMERDTIRSMLEAQQE
          PV.FL..ARQRP..E..FEEG.RRALLLKKW.LYKQR.HEMERD.IRS.LEAQQE
Retrocopy PVRFLNKARQRPQVEFLFEEGKRRALLLKKWLLYKQRKHEMERDAIRSVLEAQQE

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	7.32 RPM
SRP021940_cerebellum	0.00 RPM	24.36 RPM
SRP021940_embryo	0.00 RPM	20.41 RPM
SRP021940_placental_villous	0.00 RPM	13.57 RPM
SRP021940_synovial_membrane	0.00 RPM	13.89 RPM
SRP021940_testis	0.00 RPM	26.60 RPM

ChIP-Seq

Equus caballus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ecab_687 retrocopy.

TSS

Equus caballus was not studied using FANTOM5 data.

Lab

retro_ecab_687 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ecab_687 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Canis familiaris	retro_cfam_662

---

Parental genes homology:

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

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000001053	1 retrocopy	retro_acar_149,
Ailuropoda melanoleuca	ENSAMEG00000011421	1 retrocopy	retro_amel_257,
Callithrix jacchus	ENSCJAG00000001584	1 retrocopy	retro_cjac_3220,
Equus caballus	ENSECAG00000009876	1 retrocopy	retro_ecab_687 ,
Homo sapiens	ENSG00000185608	1 retrocopy	retro_hsap_1020,
Gorilla gorilla	ENSGGOG00000012336	1 retrocopy	retro_ggor_807,
Myotis lucifugus	ENSMLUG00000002456	1 retrocopy	retro_mluc_1950,
Macaca mulatta	ENSMMUG00000016081	1 retrocopy	retro_mmul_57,
Mustela putorius furo	ENSMPUG00000003865	1 retrocopy	retro_mputfur_394,
Nomascus leucogenys	ENSNLEG00000005372	1 retrocopy	retro_nleu_899,
Pongo abelii	ENSPPYG00000011578	1 retrocopy	retro_pabe_857,
Rattus norvegicus	ENSRNOG00000049686	1 retrocopy	retro_rnor_1624,
Tarsius syrichta	ENSTSYG00000014747	1 retrocopy	retro_tsyr_1589,