RetrogeneDB ID: retro_ecab_496

Retrocopy location

• Organism: Horse (Equus caballus)
• Coordinates: 2:74828829..74829289(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSECAG00000006610
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: CHMP4B
• Ensembl ID: ENSECAG00000008311
• Aliases: None
• Description: charged multivesicular body protein 4B [Source:HGNC Symbol;Acc:16171]

Sequence

>retro_ecab_496
AGAAAAAGGTATGAGAAGCAGCTGGCGCAGATCGACGGCACACTATCAATCATCGAGTTCCAGCGAGAGGCCCTGAAGAA
TGCCAACACCAACACCGACGTGCTCAAGAACATGGGCTATGCCTCCAAGGCCATGAAGGCTGCCCACGACAACATGGACA
TCGATAAAGTTGATGAGTTAGTGCAGGAGATTGCTAACCAGCAAGAACTTGCAGAGGAGATTTCAACAGCTATTTCAAAA
CCTGTAGGGTTTGGAGAAGGGTTTGATGAGGACGAACTCATGGCCGAATTAGAAGAACTAGAACAGGAGGAACCAGACAA
GAATTTGCTGGAAGTCAGTGGACCCGAAACAGTCCCTCTACCAAACGTTCCTTCCGTTAAGCCTACCATCAAAACCCACC
AAGAAGAAGGAAGAGGAAGACGACGACATGAAGGAATTGGAGAACTGGGTTGGATCCATT

Alignment

ORF - retro_ecab_496 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 90.26 %
• Parental protein coverage: 95.03 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  KKRYEKQLAQIDGTLSTIEFQREALENANTNTEVLKNMGYAAKAMKAAHDNMDIDKVDELMQDIADQQEL
          .KRYEKQLAQIDGTLS.IEFQREAL.NANTNT.VLKNMGYA.KAMKAAHDNMDIDKVDEL.Q.IA.QQEL
Retrocopy RKRYEKQLAQIDGTLSIIEFQREALKNANTNTDVLKNMGYASKAMKAAHDNMDIDKVDELVQEIANQQEL

Parental  AEEISTAISKPVGFGEEFDEDELMAELEELEQEELDKNLLEISGPETVPLPNVPSI-SLPSKPTKKKEEE
          AEEISTAISKPVGFGE.FDEDELMAELEELEQEE.DKNLLE.SGPETVPLPNVPS..SLPSKPTKKKEEE
Retrocopy AEEISTAISKPVGFGEGFDEDELMAELEELEQEEPDKNLLEVSGPETVPLPNVPSV>SLPSKPTKKKEEE

Parental  DDDMKELENWAGTI
          DDDMKELENW.G.I
Retrocopy DDDMKELENWVGSI

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	0.06 RPM	28.10 RPM
SRP021940_cerebellum	0.36 RPM	92.65 RPM
SRP021940_embryo	0.31 RPM	56.44 RPM
SRP021940_placental_villous	0.19 RPM	92.08 RPM
SRP021940_synovial_membrane	0.25 RPM	49.30 RPM
SRP021940_testis	0.26 RPM	67.97 RPM

ChIP-Seq

Equus caballus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ecab_496 retrocopy.

TSS

Equus caballus was not studied using FANTOM5 data.

Lab

retro_ecab_496 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ecab_496 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 15 parental genes, and 16 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000009038	1 retrocopy	retro_amel_1612,
Canis familiaris	ENSCAFG00000007478	1 retrocopy	retro_cfam_1304,
Choloepus hoffmanni	ENSCHOG00000007288	1 retrocopy	retro_chof_2518,
Equus caballus	ENSECAG00000008311	1 retrocopy	retro_ecab_496 ,
Felis catus	ENSFCAG00000025893	1 retrocopy	retro_fcat_1835,
Homo sapiens	ENSG00000101421	1 retrocopy	retro_hsap_1339,
Gorilla gorilla	ENSGGOG00000007775	1 retrocopy	retro_ggor_29,
Macaca mulatta	ENSMMUG00000008084	1 retrocopy	retro_mmul_2178,
Mustela putorius furo	ENSMPUG00000017821	2 retrocopies	retro_mputfur_1302, retro_mputfur_697,
Nomascus leucogenys	ENSNLEG00000010020	1 retrocopy	retro_nleu_1822,
Pongo abelii	ENSPPYG00000010931	1 retrocopy	retro_pabe_1111,
Pan troglodytes	ENSPTRG00000013408	1 retrocopy	retro_ptro_915,
Pteropus vampyrus	ENSPVAG00000010293	1 retrocopy	retro_pvam_973,
Rattus norvegicus	ENSRNOG00000046585	1 retrocopy	retro_rnor_61,
Tarsius syrichta	ENSTSYG00000013212	1 retrocopy	retro_tsyr_1453,