RetrogeneDB ID: retro_ecab_556

Retrocopy location

• Organism: Horse (Equus caballus)
• Coordinates: 20:37146915..37147198(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: TM2D1
• Ensembl ID: ENSECAG00000015035
• Aliases: None
• Description: TM2 domain containing 1 [Source:HGNC Symbol;Acc:24142]

Sequence

>retro_ecab_556
CATCTGATTGGAAATAAAGTTCATTTTCTCAAGCCTATATCTTGTCAAAATGTCAAAACAACTACTCATATAAAGCAGCA
GTTGCACTGTCTTTTTCTCGGACAGTCAGCAGCAGATTGATTTTCCCTTGGATGCTCTGCCTTGGGCTGTTGACGGTTTG
CACTGGAGGGTTTTGTGGATCGGGAGCTTAACTTATTTCATTCTTACTTCAATGCAGACTGTTGGACCTTCAGACGGAAG
TGGTTATGTTACAGATTATTATGGAACCAGACTTACAAGACTA

Alignment

ORF - retro_ecab_556 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 60.82 %
• Parental protein coverage: 55.23 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  HFTGREVGFFKPISCRNVNGYSYKVAVALSLFLGWLGADRFYLGYPALG-LLKFCTVGFCG-IGSLIDFI
          H..G..V.F.KPISC.NV............LFLG...AD.F.LG..ALG.LL..CT.GFCG.IGSL..FI
Retrocopy HLIGNKVHFLKPISCQNVKTTTHIKQQLHCLFLGQSAAD*FSLGCSALG<LLTVCTGGFCG<IGSLTYFI

Parental  LISMQIVGPSDGSSYIIDYYGTRLTRL
          L.SMQ.VGPSDGS.Y..DYYGTRLTRL
Retrocopy LTSMQTVGPSDGSGYVTDYYGTRLTRL

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	13.10 RPM
SRP021940_cerebellum	0.05 RPM	19.21 RPM
SRP021940_embryo	0.10 RPM	8.77 RPM
SRP021940_placental_villous	0.00 RPM	18.19 RPM
SRP021940_synovial_membrane	0.03 RPM	9.91 RPM
SRP021940_testis	0.00 RPM	25.90 RPM

ChIP-Seq

Equus caballus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ecab_556 retrocopy.

TSS

Equus caballus was not studied using FANTOM5 data.

Lab

retro_ecab_556 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ecab_556 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 10 parental genes, and 13 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000011705	1 retrocopy	retro_amel_1290,
Canis familiaris	ENSCAFG00000018838	1 retrocopy	retro_cfam_1213,
Choloepus hoffmanni	ENSCHOG00000013535	1 retrocopy	retro_chof_1494,
Cavia porcellus	ENSCPOG00000012287	1 retrocopy	retro_cpor_471,
Equus caballus	ENSECAG00000015035	1 retrocopy	retro_ecab_556 ,
Erinaceus europaeus	ENSEEUG00000001567	1 retrocopy	retro_eeur_708,
Loxodonta africana	ENSLAFG00000013979	1 retrocopy	retro_lafr_662,
Mus musculus	ENSMUSG00000028563	2 retrocopies	retro_mmus_1412, retro_mmus_1981,
Rattus norvegicus	ENSRNOG00000007527	1 retrocopy	retro_rnor_1104,
Tupaia belangeri	ENSTBEG00000002089	3 retrocopies	retro_tbel_1156, retro_tbel_1730, retro_tbel_201,