RetrogeneDB ID: retro_ecab_618

Retrocopy location

• Organism: Horse (Equus caballus)
• Coordinates: 23:28823260..28823683(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: C1orf43
• Ensembl ID: ENSECAG00000017585
• Aliases: None
• Description: chromosome 1 open reading frame 43 [Source:HGNC Symbol;Acc:29876]

Sequence

>retro_ecab_618
GGAAGACAATGCCCCAAATTCCTGAAGGAGGAAATTGACACTCAACTCTCCAGGAAACAGGATGTCAAGCATTAACCCGA
GCTCTTGCAGATTAAGACGGCAGTTTGCTCCAGCGGGAGACCCAGGGAAATCAATACTGCAAAAATTACCTCTACAGCAC
AAAAACACTGGCCAGCAAAAGTGCCTTTGAGATCCCACTTCATGCTGTAGATCAGCAGCTCCATTTCCTAATGAGCGAGC
ATTTCAGCTCCTACTTAGATCTCTGAAACACTTGTATCCTTTCAAAAGAGCCTGCAAGGCCCTCCTTGATATCCTGCTAG
ATGGCTATGAATCAGCCTGCTCTGGGAAGGAGTCTGTGTCCAGAGTGAGCACTTGTTCTTTCAGGAAGCAGAGTGTGAGT
TGACTGAGACAATCGAGGCACAG

Alignment

ORF - retro_ecab_618 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 54.11 %
• Parental protein coverage: 56.52 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  GHNAPKDLKEEIDIRLSRVQDIKYEPQLL-ADDDARLLQLETQGNQNCYNYLYRMKALDAIRASEIPFHA
          G...PK.LKEEID..LSR.QD.K..P.LL.AD.D..LLQ.ETQGNQ.C.NYLY..K.L....A.EIP.HA
Retrocopy GRQCPKFLKEEIDTQLSRKQDVKH*PELL<AD*DGSLLQRETQGNQYCKNYLYSTKTLASKSAFEIPLHA

Parental  DGRHPCSLMGKNFRSYLLDLRNSST-PFKGVRKALIDTLLDGYETARYG-TGVFGQSEYLRYQEALSELA
          .......LM...F.SY.LDL.N....PFK...KAL.D.LLDGYE.A..G..GV..QSE.L..QEA..EL.
Retrocopy VDQQLHFLMSEHFSSY-LDL*NTCI<PFKRACKALLDILLDGYESACSG<EGVCVQSEHLFFQEAECELT

Parental  TVVKAR
          ....A.
Retrocopy ETIEAQ

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	19.48 RPM
SRP021940_cerebellum	0.00 RPM	37.34 RPM
SRP021940_embryo	0.00 RPM	26.14 RPM
SRP021940_placental_villous	0.00 RPM	30.60 RPM
SRP021940_synovial_membrane	0.00 RPM	20.64 RPM
SRP021940_testis	0.00 RPM	77.56 RPM

ChIP-Seq

Equus caballus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ecab_618 retrocopy.

TSS

Equus caballus was not studied using FANTOM5 data.

Lab

retro_ecab_618 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ecab_618 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 13 parental genes, and 36 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000011865	1 retrocopy	retro_amel_190,
Callithrix jacchus	ENSCJAG00000009722	1 retrocopy	retro_cjac_175,
Dasypus novemcinctus	ENSDNOG00000019160	1 retrocopy	retro_dnov_2515,
Equus caballus	ENSECAG00000017585	2 retrocopies	retro_ecab_618 , retro_ecab_814,
Echinops telfairi	ENSETEG00000001056	15 retrocopies	retro_etel_1138, retro_etel_1318, retro_etel_1388, retro_etel_1633, retro_etel_2182, retro_etel_2205, retro_etel_2206, retro_etel_394, retro_etel_651, retro_etel_719, retro_etel_720, retro_etel_773, retro_etel_842, retro_etel_957, retro_etel_981,
Macropus eugenii	ENSMEUG00000002600	6 retrocopies	retro_meug_1149, retro_meug_1298, retro_meug_1439, retro_meug_1637, retro_meug_213, retro_meug_69,
Myotis lucifugus	ENSMLUG00000013338	1 retrocopy	retro_mluc_537,
Monodelphis domestica	ENSMODG00000017237	3 retrocopies	retro_mdom_1283, retro_mdom_2003, retro_mdom_323,
Otolemur garnettii	ENSOGAG00000012008	2 retrocopies	retro_ogar_2563, retro_ogar_38,
Pteropus vampyrus	ENSPVAG00000002717	1 retrocopy	retro_pvam_696,
Rattus norvegicus	ENSRNOG00000017758	1 retrocopy	retro_rnor_139,
Sarcophilus harrisii	ENSSHAG00000012915	1 retrocopy	retro_shar_740,
Tursiops truncatus	ENSTTRG00000015824	1 retrocopy	retro_ttru_923,