RetrogeneDB ID: retro_ptro_1753

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 2B:241650451..241651320(-)
• Located in intron of: ENSPTRG00000013070

Retrocopy information

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

Parental gene information

• Parental gene symbol: RPL3L
• Ensembl ID: ENSPTRG00000007617
• Aliases: None
• Description: ribosomal protein L3-like [Source:HGNC Symbol;Acc:10351]

Sequence

>retro_ptro_1753
CCTCAAGGCCTCCAGACCTTCAAGACCGTCTTCGCTAAGTACATCAGCGATGAGTGCAAAAAGCACTTCTCTAACAACTG
GCATAAATCTAAGAGGAAGGCCTTTACCAGTTACTGCAAGAAATGGCAGAATAAGGATGGCAAGAAGCAGCTGGAGCAGG
ACTTCAGCAGCATGAAGAAGCACTGCCAAGTCATCCATGTCACTGCCACACCCACATATACCTGCTTCCTCCATGCCAGA
AGAAGGCCCCGCTGATGGAGATCCAGATGAACAGAGGCACCATGGCCAAGAAGCTGGACTGGGGCCGGGAGAGGCTAGAG
CAGCCCATACCTGTGAACCAAGTCTTTGGGCAGGATGAGATGATTGACGTCTTCAAGGTGACCAAGGGCAAAGACTACAA
AGGGGTCACAAGTCATTGACACACCAAGAAGCTACCCTGCAAGACCCACTGAGGCTTGTGCAAGGTGGCCTGGATTGGGT
CATGGCATCCTGCCTGTGTGGCCTTCTCTGTGGCACGTGCTGGGCAGAAAGGCTACCATCACCACACTGAGATCACAAGA
AGATTGATCTCTAAGATCGGCCAGGGCTACGTTATCAAGGATGACAAACTGATCAAGAACAATGCCTCCACTGACCATGA
CCTGCCTGACAAAAGTATCAACTCTCTGGGTGGCTTTGTCCCATATGGTGAAGTGACCAGTGGCTTTGTCATGCTGAAGG
AATGTGTGGTGGGAACCAAGAAGTGAGTGCTCACCCTCCACAAGTCTTTGCTGGCTGAGACCAAATGGCGGGCTCTGGAG
AAGACTGACCTTAAGTTCATTGACACCACTGCCAAGTTTGGCCATGGCTGCTCCCAGACCATGGAAGAG

Alignment

ORF - retro_ptro_1753 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 59.11 %
• Parental protein coverage: 71.01 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  PRGLRSFKTIFAEHLSDECRRRFYKDWHKSKKKAFTKACKRWRDTDGKKQLQKDFAAMKKYCKVIRVIV-
          P.GL..FKT.FA...SDEC...F...WHKSK.KAFT..CK.W...DGKKQL..DF..MKK.C.VI.V...
Retrocopy PQGLQTFKTVFAKYISDECKKHFSNNWHKSKRKAFTSYCKKWQNKDGKKQLEQDFSSMKKHCQVIHVTA<

Parental  HTQMKLLPFRQKKAHIMEIQLNGGTVAEKVAWAQARLEKQVPVHSVFSQSEVIDVIAVTKGRGVKGVTSR
          HT...LLP..QKKA..MEIQ.N.GT.A.K..W...RLE...PV..VF.Q.E.IDV..VTKG...KGVTS.
Retrocopy HTHIYLLPPCQKKAPLMEIQMNRGTMAKKLDWGRERLEQPIPVNQVFGQDEMIDVFKVTKGKDYKGVTSH

Parental  WHTKKLPRKTHKGLRKVACIGAWHPARVGCSIARAGQKGYHHRTELNKK-IFRIGRGPHMEDGKPVKNNA
          .HTKKLP.KTH.GL.KVA.IG.WHPA.V..S.ARAGQKGYHH.TE.....I..IG.G....D.K..KNNA
Retrocopy *HTKKLPCKTH*GLCKVAWIGSWHPACVAFSVARAGQKGYHHHTEITRRLISKIGQGYVIKDDKLIKNNA

Parental  STSYDVTAKSITPLGGFPHYGEVNNDFVMLKGCIAGTKKRVITLRKSLLVHHSRQAVENIELKFIDTTSK
          ST..D...KSI..LGGF..YGEV...FVMLK.C..GTKK.V.TL.KSLL......A.E...LKFIDTT.K
Retrocopy STDHDLPDKSINSLGGFVPYGEVTSGFVMLKECVVGTKK*VLTLHKSLLAETKWRALEKTDLKFIDTTAK

Parental  FGHGRFQTAQE
          FGHG..QT..E
Retrocopy FGHGCSQTMEE

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	0.05 RPM	0.02 RPM
SRP007412_cerebellum	0.00 RPM	0.00 RPM
SRP007412_heart	0.00 RPM	38.27 RPM
SRP007412_kidney	0.08 RPM	0.00 RPM
SRP007412_liver	0.00 RPM	0.03 RPM
SRP007412_testis	0.00 RPM	0.84 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_1753 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_1753 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_1753 has 4 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_2403
Gorilla gorilla	retro_ggor_1822
Pongo abelii	retro_pabe_2167
Macaca mulatta	retro_mmul_973

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Parental genes homology:

Parental genes homology involve 5 parental genes, and 25 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000008489	1 retrocopy	retro_amel_1881,
Nomascus leucogenys	ENSNLEG00000008850	9 retrocopies	retro_nleu_1107, retro_nleu_1130, retro_nleu_1249, retro_nleu_1305, retro_nleu_1673, retro_nleu_1824, retro_nleu_2046, retro_nleu_2060, retro_nleu_3126,
Pongo abelii	ENSPPYG00000006973	1 retrocopy	retro_pabe_2854,
Pan troglodytes	ENSPTRG00000007617	12 retrocopies	retro_ptro_1439, retro_ptro_1473, retro_ptro_1753 , retro_ptro_2150, retro_ptro_2339, retro_ptro_2462, retro_ptro_2501, retro_ptro_2646, retro_ptro_2741, retro_ptro_2767, retro_ptro_3163, retro_ptro_916,
Ictidomys tridecemlineatus	ENSSTOG00000012921	2 retrocopies	retro_itri_1344, retro_itri_867,