RetrogeneDB ID: retro_ecab_302

Retrocopy location

• Organism: Horse (Equus caballus)
• Coordinates: 14:90992749..90992962(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PAM16
• Ensembl ID: ENSECAG00000019387
• Aliases: None
• Description: presequence translocase-associated motor 16 homolog (S. cerevisiae) [Source:HGNC Symbol;Acc:29679]

Sequence

>retro_ecab_302
GCCTCAGTTTCCTTATCTGTAAAGCAAGGGGTTATCAACGTCTCCAAGCTCAGCCCCAAGGAGGGGAGCTACAAACATTT
ATTTGAGGTGAGTGATGAATCCGTGGGTGGCTTCTACGTGCAGACAAATGTGGTTCGAGTGAAGGAGCGGCCCGATGAGG
AACTCAGAATCCAGGCCCGAGAGGACAGAAACAAAGGGCAGATGCCGGAAACA

Alignment

ORF - retro_ecab_302 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 59.46 %
• Parental protein coverage: 59.2 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  SGLSLQEAQQILNVSKLSPEEIQKNYEHLFKVNDKSVGGSFYLQSKVVRAKERLDEELRIQAQEDREREQ
          ...SL...Q...NVSKLSP.E....Y.HLF.V.D.SVGG.FY.Q..VVR.KER.DEELRIQA.EDR...Q
Retrocopy ASVSLSVKQGVINVSKLSPKE--GSYKHLFEVSDESVGG-FYVQTNVVRVKERPDEELRIQAREDRNKGQ

Parental  TPPT
          .P.T
Retrocopy MPET

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	7.85 RPM
SRP021940_cerebellum	0.00 RPM	13.50 RPM
SRP021940_embryo	0.00 RPM	10.89 RPM
SRP021940_placental_villous	0.00 RPM	5.68 RPM
SRP021940_synovial_membrane	0.00 RPM	6.42 RPM
SRP021940_testis	0.00 RPM	47.38 RPM

ChIP-Seq

Equus caballus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ecab_302 retrocopy.

TSS

Equus caballus was not studied using FANTOM5 data.

Lab

retro_ecab_302 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ecab_302 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 16 parental genes, and 29 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000009200	1 retrocopy	retro_btau_1664,
Canis familiaris	ENSCAFG00000019226	1 retrocopy	retro_cfam_1967,
Callithrix jacchus	ENSCJAG00000019772	1 retrocopy	retro_cjac_1148,
Dasypus novemcinctus	ENSDNOG00000010921	2 retrocopies	retro_dnov_1361, retro_dnov_8,
Dipodomys ordii	ENSDORG00000014888	1 retrocopy	retro_dord_81,
Equus caballus	ENSECAG00000019387	1 retrocopy	retro_ecab_302 ,
Erinaceus europaeus	ENSEEUG00000007432	7 retrocopies	retro_eeur_138, retro_eeur_171, retro_eeur_213, retro_eeur_234, retro_eeur_273, retro_eeur_440, retro_eeur_673,
Echinops telfairi	ENSETEG00000006416	1 retrocopy	retro_etel_2070,
Felis catus	ENSFCAG00000027971	1 retrocopy	retro_fcat_520,
Myotis lucifugus	ENSMLUG00000008921	6 retrocopies	retro_mluc_2446, retro_mluc_2447, retro_mluc_2448, retro_mluc_2516, retro_mluc_2517, retro_mluc_429,
Mus musculus	ENSMUSG00000014301	1 retrocopy	retro_mmus_73,
Rattus norvegicus	ENSRNOG00000004608	1 retrocopy	retro_rnor_713,
Sus scrofa	ENSSSCG00000007947	2 retrocopies	retro_sscr_1090, retro_sscr_468,
Ictidomys tridecemlineatus	ENSSTOG00000003461	1 retrocopy	retro_itri_1732,
Tupaia belangeri	ENSTBEG00000001347	1 retrocopy	retro_tbel_3190,
Tarsius syrichta	ENSTSYG00000009306	1 retrocopy	retro_tsyr_282,