RetrogeneDB ID: retro_pabe_857

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 12:67535975..67536514(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MRPL40
• Ensembl ID: ENSPPYG00000011578
• Aliases: None
• Description: mitochondrial ribosomal protein L40 [Source:HGNC Symbol;Acc:14491]

Sequence

>retro_pabe_857
CAGGTTTGAGGCACCCACCAGCGAGCTTCAGTGTTGTCCTCCTAGGAACTCATTCCTGTGAGAGCAGAACCTCTTCAAGA
GCAGAAGGTGAATCCTAAAAATGACCAAGCAGGAAAGGGCTGCTTGAAAAACAAGATATGAAAACTGGAAAAGGCTAGCC
AAGAGCTCATTCTTGTTGCAGATTTTATTAGCCTTGTGAGGTTCTTGGATAAAGCAAGCCAGTGGCCTCAGGTGGAGCTC
TCCTTGGAGGAGAGTGAGTGGAGAGCTCTGCTTCTGATGAGTGGTCTCTGTACAAGCAGCGAGAGTACACTATGGACAGG
GACACCATCAAGGCTGTGCTGGGGACCCAGCAGGAAGCTCTGCAGGAGCTACCACTCGAGTCCCCTGAGTTCCCCACTGA
GACCATCAAGTGGGACCACAGCATGTTCCCCTTTGAGTGGGAAGGTCCAGATTACACACTATGGGTCTCTAACTACCAGC
CCCCCAAAGGCAGGTACAATGACATCACCAAGATGTACACACAGGTAGAGCTCAAGAGA

Alignment

ORF - retro_pabe_857 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 63.74 %
• Parental protein coverage: 96.28 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  QIRETHQRASLLSFWELIPMRSEPLRKKKKVDPKKDQEAKERLKRKIRKLEKAAQELIPIEDFITPLKFL
          Q...THQRAS.LS..ELIP.R.EPL...K.V.PK.DQ..K..LK.KI.KLEKA.QELI...DFI....FL
Retrocopy QV*GTHQRASVLSS*ELIPVRAEPLQEQK-VNPKNDQAGKGCLKNKI*KLEKASQELILVADFISLVRFL

Parental  DKARERPQVELTFEETERRALLLK-KWSLYKQQEHKMERDTIRAMLEAQQEALEELRLESPKLHAEAIKR
          DKA...PQVEL..EE.E.RALLL...WSLYKQ.E..M.RDTI.A.L..QQEAL.EL.LESP....E.IK.
Retrocopy DKASQWPQVELSLEESEWRALLLM<EWSLYKQREYTMDRDTIKAVLGTQQEALQELPLESPEFPTETIKW

Parental  DPNLFPFEKEGPHYTPPIPNYQPPEGRYNDITKVYTQVEFKR
          D...FPFE.EGP.YT....NYQPP.GRYNDITK.YTQVE.KR
Retrocopy DHSMFPFEWEGPDYTLWVSNYQPPKGRYNDITKMYTQVELKR

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
SRP007412_brain_prefrontal_cortex	0.06 RPM	14.15 RPM
SRP007412_cerebellum	0.12 RPM	18.48 RPM
SRP007412_heart	0.03 RPM	19.42 RPM
SRP007412_kidney	0.07 RPM	29.40 RPM
SRP007412_liver	0.06 RPM	41.56 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_857 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_857 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_857 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_1020
Gorilla gorilla	retro_ggor_807
Callithrix jacchus	retro_cjac_3220

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Parental genes homology:

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

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000001053	1 retrocopy	retro_acar_149,
Ailuropoda melanoleuca	ENSAMEG00000011421	1 retrocopy	retro_amel_257,
Callithrix jacchus	ENSCJAG00000001584	1 retrocopy	retro_cjac_3220,
Equus caballus	ENSECAG00000009876	1 retrocopy	retro_ecab_687,
Homo sapiens	ENSG00000185608	1 retrocopy	retro_hsap_1020,
Gorilla gorilla	ENSGGOG00000012336	1 retrocopy	retro_ggor_807,
Myotis lucifugus	ENSMLUG00000002456	1 retrocopy	retro_mluc_1950,
Macaca mulatta	ENSMMUG00000016081	1 retrocopy	retro_mmul_57,
Mustela putorius furo	ENSMPUG00000003865	1 retrocopy	retro_mputfur_394,
Nomascus leucogenys	ENSNLEG00000005372	1 retrocopy	retro_nleu_899,
Pongo abelii	ENSPPYG00000011578	1 retrocopy	retro_pabe_857 ,
Rattus norvegicus	ENSRNOG00000049686	1 retrocopy	retro_rnor_1624,
Tarsius syrichta	ENSTSYG00000014747	1 retrocopy	retro_tsyr_1589,