RetrogeneDB ID: retro_ptro_2417

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 6:10545841..10546471(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MRPL48
• Ensembl ID: ENSPTRG00000004049
• Aliases: None
• Description: Pan troglodytes mitochondrial ribosomal protein L48 (MRPL48), nuclear gene encoding mitochondrial protein, mRNA. [Source:RefSeq mRNA;Acc:NM_001251970]

Sequence

>retro_ptro_2417
ATGAGCAGAACCTTGGAAAAAGTGCTGTGCCTGAGGAACAATACCATTTTTAAGCAAGGCTTTTCACTCTTAAGGCTTAG
AACTTCAGCAGAGAAGCCCATCTATTCTGTAGGTGGCATTCTACTAAGTACCAGTCCGCCCTACAAGACAAAGCCCACCC
ACGCCATTGGAAAGTACAAGCACCTAATTAAAGCAGAAGAGCCCGAGAAGAAGCGAAAAGTGGAAGTGAAACTCATTAAT
TTGGGGACAGATGATGAATATGGGGTTTTAAACATTCACCTGCCTGCATATGACATGACCCTGGCAGAGAGTTATGCCCA
GTATGTTCACAACTTCTGCAACTCTCTCTCCATTAAAGTCGAGGAAAGTTATGTGATGCCAACCAAAACCACTGAAGTGT
TGTGGTTGCAGGACCAAGGCAGCAAAACGTTCCTGGACTCAGTGCTTACCACCCATGAGCGAGTGGTTCAGATGAGCAGT
TTGAGTGCTATGTTTGCAGAGATTTTCTTGGAAATAATCCAAAGCAGTCTTCCTGAAGGAGTCAGATTGTCAGTGAAGGA
GCACACTGAAGAAGACTTCAAGGGAAGATTCAAAGCTCGACCAGAACTGGAAGAACGGTTGGCTGAGTTG

Alignment

ORF - retro_ptro_2417 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 88.15 %
• Parental protein coverage: 99.53 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MSGTLEKMLCLRNNTIFKQAFSLLRFRTSGEKPIYSVGGILLSISRPYKTKPTHGIGKYKHLIKAEEPKK
          MS.TLEK.LCLRNNTIFKQ.FSLLR.RTS.EKPIYSVGGILLS.S.PYKTKPTH.IGKYKHLIKAEEP.K
Retrocopy MSRTLEKVLCLRNNTIFKQGFSLLRLRTSAEKPIYSVGGILLSTSPPYKTKPTHAIGKYKHLIKAEEPEK

Parental  KKGKVEVRAINLGTDYEYGVLNIHLTAYDMTLAESYAQYVHNLCNSLSIKVEESYAMPTKTIEVLQLQDQ
          K..KVEV..INLGTD.EYGVLNIHL.AYDMTLAESYAQYVHN.CNSLSIKVEESY.MPTKT.EVL.LQDQ
Retrocopy KR-KVEVKLINLGTDDEYGVLNIHLPAYDMTLAESYAQYVHNFCNSLSIKVEESYVMPTKTTEVLWLQDQ

Parental  GSKMFLDSVLTTHERVVQISGLSATFAEIFLEIIQSSLPEGVRLSVKEHTEEDFKGRFKARPELEELLAK
          GSK.FLDSVLTTHERVVQ.S.LSA.FAEIFLEIIQSSLPEGVRLSVKEHTEEDFKGRFKARPELEE.LA.
Retrocopy GSKTFLDSVLTTHERVVQMSSLSAMFAEIFLEIIQSSLPEGVRLSVKEHTEEDFKGRFKARPELEERLAE

Parental  L
          L
Retrocopy L

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	0.00 RPM	19.41 RPM
SRP007412_cerebellum	0.00 RPM	18.07 RPM
SRP007412_heart	0.00 RPM	12.91 RPM
SRP007412_kidney	0.00 RPM	18.91 RPM
SRP007412_liver	0.00 RPM	7.86 RPM
SRP007412_testis	0.00 RPM	16.55 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_2417 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_2417 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_2417 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_3557

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Parental genes homology:

Parental genes homology involve 10 parental genes, and 12 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000005585	1 retrocopy	retro_cfam_1437,
Homo sapiens	ENSG00000175581	1 retrocopy	retro_hsap_3557,
Mustela putorius furo	ENSMPUG00000009716	1 retrocopy	retro_mputfur_38,
Mus musculus	ENSMUSG00000030706	2 retrocopies	retro_mmus_2478, retro_mmus_563,
Nomascus leucogenys	ENSNLEG00000017097	1 retrocopy	retro_nleu_1376,
Oryctolagus cuniculus	ENSOCUG00000009302	1 retrocopy	retro_ocun_39,
Otolemur garnettii	ENSOGAG00000004771	1 retrocopy	retro_ogar_234,
Pan troglodytes	ENSPTRG00000004049	1 retrocopy	retro_ptro_2417 ,
Tursiops truncatus	ENSTTRG00000005403	2 retrocopies	retro_ttru_1123, retro_ttru_297,
Vicugna pacos	ENSVPAG00000004657	1 retrocopy	retro_vpac_538,