RetrogeneDB ID: retro_ptro_1270

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 18:56626167..56626529(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CCDC59
• Ensembl ID: ENSPTRG00000005266
• Aliases: None
• Description: None

Sequence

>retro_ptro_1270
AAAGTTGTCCAGCCTTTGCTAGAGAACAATGCAGTATTACCTAATGTTGGTCGGAAGAACACTTCACCATTGAGCAGCTT
CAGCCAGAAGAGCAATGTAGCAAAATGGGTAAACTCCATTACCATTCAAAAAACAAAAAATGAAAGAAACATCAAGTCGC
AAAGCACGAGCAGAATGTGAATAAGTAGAAGCTAAGCATGCTGCTAAGAAACAAGAACGTGAGAGGATAAAATGAAAAAG
AAAAGCTCAAAGGCTCCTAAGCAAAGAAAATGCAAGTGTTCCAAATATTGAGCAAAAAGACAAGAAAGGGCCAACCAAAC
TTGAACTTATACATGGAGTATCTTCTTCATAAAATACATAAA

Alignment

ORF - retro_ptro_1270 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 53.17 %
• Parental protein coverage: 50.62 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  QVHQPLLE-EQCSIDQPLFEDQCSFDQPQPEEQCIGT-VNSFTIPKKNK-KKTSNQKAQEEYEQVQAKRA
          .V.QPLLE.EQCSI.....E......Q.QPEEQC....VNS.TI......K.TS..KA..E.E.V.AK.A
Retrocopy KVVQPLLE<EQCSIT*CWSEEHFTIEQLQPEEQCSKM>VNSITIXXXXX>KETSSRKARAECE*VEAKHA

Parental  AKKQEFERRKQEREEAQRLYKKKKMEVFKILNKKTK-KGQPNLNVQMEYLLQKIQE
          AKKQE.ER.K..R..AQRL..K....V..I...K.K.KGQPNLN..MEYLL.KI..
Retrocopy AKKQERERIK*KR-KAQRLLSKENASVPNI-EQKDK>KGQPNLNLYMEYLLHKIHK

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	5.13 RPM
SRP007412_cerebellum	0.00 RPM	9.93 RPM
SRP007412_heart	0.00 RPM	10.67 RPM
SRP007412_kidney	0.00 RPM	10.75 RPM
SRP007412_liver	0.00 RPM	10.97 RPM
SRP007412_testis	0.00 RPM	40.78 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_1270 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_1270 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_1270 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 12 parental genes, and 27 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000016875	1 retrocopy	retro_amel_954,
Bos taurus	ENSBTAG00000036282	4 retrocopies	retro_btau_725, retro_btau_726, retro_btau_727, retro_btau_728,
Choloepus hoffmanni	ENSCHOG00000007788	1 retrocopy	retro_chof_1648,
Dasypus novemcinctus	ENSDNOG00000011546	1 retrocopy	retro_dnov_1033,
Dipodomys ordii	ENSDORG00000003005	1 retrocopy	retro_dord_485,
Echinops telfairi	ENSETEG00000000256	2 retrocopies	retro_etel_1338, retro_etel_1789,
Gorilla gorilla	ENSGGOG00000025296	2 retrocopies	retro_ggor_1386, retro_ggor_99,
Microcebus murinus	ENSMICG00000000967	4 retrocopies	retro_mmur_1456, retro_mmur_354, retro_mmur_689, retro_mmur_909,
Oryctolagus cuniculus	ENSOCUG00000017824	2 retrocopies	retro_ocun_1782, retro_ocun_498,
Otolemur garnettii	ENSOGAG00000004383	1 retrocopy	retro_ogar_2065,
Pan troglodytes	ENSPTRG00000005266	1 retrocopy	retro_ptro_1270 ,
Tupaia belangeri	ENSTBEG00000008887	7 retrocopies	retro_tbel_1515, retro_tbel_2047, retro_tbel_2126, retro_tbel_302, retro_tbel_3391, retro_tbel_3721, retro_tbel_972,