RetrogeneDB ID: retro_ecab_752

Retrocopy location

• Organism: Horse (Equus caballus)
• Coordinates: 30:23478608..23478790(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: FKBP1B
• Ensembl ID: ENSECAG00000015664
• Aliases: None
• Description: FK506 binding protein 1B, 12.6 kDa [Source:HGNC Symbol;Acc:3712]

Sequence

>retro_ecab_752
ACCTTTGCAAAGCTCCACCAGACATGCGTGGTGCATACAGCAGGATGCTTCAAGATGGAAAGAAATTTGATTCTTCCCAG
GATGGAAACAAGACAATTAAGTTTATGGTAGGCAAGCAGGAGGTGATCCGAGTCTAGGAAGGTGTGACCCAGATGAGGAT
GGGCCAGAGAGCTAAACTATCT

Alignment

ORF - retro_ecab_752 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 65.08 %
• Parental protein coverage: 64.58 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  TFPKKGQTCVVH-YTGMLQNGKKFDSSRDRNKPFKFRIGKQEVIKGFEEGAAQMSLGQRAKLT
          TF.K..QTCVVH.Y..MLQ.GKKFDSS.D.NK..KF..GKQEVI....EG..QM..GQRAKL.
Retrocopy TFAKLHQTCVVH<YSRMLQDGKKFDSSQDGNKTIKFMVGKQEVIR-V*EGVTQMRMGQRAKLS

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	1.24 RPM
SRP021940_cerebellum	0.00 RPM	22.38 RPM
SRP021940_embryo	0.00 RPM	10.51 RPM
SRP021940_placental_villous	0.00 RPM	0.67 RPM
SRP021940_synovial_membrane	0.00 RPM	2.09 RPM
SRP021940_testis	0.00 RPM	1.02 RPM

ChIP-Seq

Equus caballus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ecab_752 retrocopy.

TSS

Equus caballus was not studied using FANTOM5 data.

Lab

retro_ecab_752 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ecab_752 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 10 parental genes, and 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000007700	1 retrocopy	retro_cjac_696,
Ciona savignyi	ENSCSAVG00000006859	1 retrocopy	retro_csav_11,
Equus caballus	ENSECAG00000015664	1 retrocopy	retro_ecab_752 ,
Equus caballus	ENSECAG00000018299	2 retrocopies	retro_ecab_352, retro_ecab_565,
Homo sapiens	ENSG00000119782	1 retrocopy	retro_hsap_1329,
Macropus eugenii	ENSMEUG00000010689	1 retrocopy	retro_meug_14,
Macaca mulatta	ENSMMUG00000012341	1 retrocopy	retro_mmul_2171,
Nomascus leucogenys	ENSNLEG00000000800	1 retrocopy	retro_nleu_1406,
Pongo abelii	ENSPPYG00000012604	1 retrocopy	retro_pabe_1105,
Pan troglodytes	ENSPTRG00000011708	1 retrocopy	retro_ptro_906,