RetrogeneDB ID: retro_ecab_940

Retrocopy location

• Organism: Horse (Equus caballus)
• Coordinates: 7:85423425..85423722(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PDZD11
• Ensembl ID: ENSECAG00000010771
• Aliases: None
• Description: PDZ domain containing 11 [Source:HGNC Symbol;Acc:28034]

Sequence

>retro_ecab_940
AGGGTATACCGTGCATGCTGCAACAATGAGTTGAGCCATTTTCTGCCCCGAATCATCACACTGAAGAAGCCCCCTGGAGC
TCAGTGGGGATTTAACATCCGAGGACGAAAGGCCTCACAGCTGAGCATCTTCATCTCCACGGTGATTCCTGGCTCTGAGG
CACACTGAGCAGGACTTCAGGAAGGGAACCAAGTCCTAGCTGTGAATGATGTGGATTTCCAAGATCTTGAGCATAGCAAG
GCTGTGGAGATCCTGAAGACAACCCACGAAATCAGCATGCATGCATGTCTCCTTCCT

Alignment

ORF - retro_ecab_940 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 76.77 %
• Parental protein coverage: 70.71 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  RVYHPDYNNELTQFLPRIVTLKKPPGAQLGFNIRGGKASQLGIFISKVIPDSDAHRAGLQEGDQVLAVND
          RVY....NNEL..FLPRI.TLKKPPGAQ.GFNIRG.KASQL.IFIS.VIP.S.AH.AGLQEG.QVLAVND
Retrocopy RVYRACCNNELSHFLPRIITLKKPPGAQWGFNIRGRKASQLSIFISTVIPGSEAH*AGLQEGNQVLAVND

Parental  VDFQDIEHSKAVEILKTAREISMRVRFFP
          VDFQD.EHSKAVEILKT..EISM.....P
Retrocopy VDFQDLEHSKAVEILKTTHEISMHACLLP

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	7.20 RPM
SRP021940_cerebellum	0.00 RPM	23.63 RPM
SRP021940_embryo	0.08 RPM	23.42 RPM
SRP021940_placental_villous	0.00 RPM	22.32 RPM
SRP021940_synovial_membrane	0.00 RPM	12.60 RPM
SRP021940_testis	0.06 RPM	11.57 RPM

ChIP-Seq

Equus caballus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ecab_940 retrocopy.

TSS

Equus caballus was not studied using FANTOM5 data.

Lab

retro_ecab_940 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ecab_940 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Bos taurus	retro_btau_594

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Parental genes homology:

Parental genes homology involve 17 parental genes, and 20 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000009203	1 retrocopy	retro_amel_158,
Canis familiaris	ENSCAFG00000028800	1 retrocopy	retro_cfam_1549,
Callithrix jacchus	ENSCJAG00000012432	1 retrocopy	retro_cjac_138,
Equus caballus	ENSECAG00000010771	1 retrocopy	retro_ecab_940 ,
Echinops telfairi	ENSETEG00000008626	3 retrocopies	retro_etel_1026, retro_etel_1863, retro_etel_921,
Homo sapiens	ENSG00000120509	1 retrocopy	retro_hsap_1439,
Gorilla gorilla	ENSGGOG00000006626	1 retrocopy	retro_ggor_1108,
Macropus eugenii	ENSMEUG00000012040	1 retrocopy	retro_meug_1858,
Macaca mulatta	ENSMMUG00000013938	1 retrocopy	retro_mmul_2265,
Mustela putorius furo	ENSMPUG00000004220	1 retrocopy	retro_mputfur_823,
Nomascus leucogenys	ENSNLEG00000000863	1 retrocopy	retro_nleu_1414,
Otolemur garnettii	ENSOGAG00000016423	1 retrocopy	retro_ogar_2975,
Pongo abelii	ENSPPYG00000020929	1 retrocopy	retro_pabe_1193,
Pan troglodytes	ENSPTRG00000021995	1 retrocopy	retro_ptro_981,
Sarcophilus harrisii	ENSSHAG00000005380	1 retrocopy	retro_shar_149,
Tupaia belangeri	ENSTBEG00000002767	2 retrocopies	retro_tbel_3155, retro_tbel_3203,
Tursiops truncatus	ENSTTRG00000007864	1 retrocopy	retro_ttru_953,