RetrogeneDB ID: retro_ptro_1729

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 2B:197921257..197921813(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: DNAJC17
• Ensembl ID: ENSPTRG00000006929
• Aliases: None
• Description: None

Sequence

>retro_ptro_1729
AGCACCAGGACACTAGAGCGAGAGATCAAATGCCTGAGTGAAGAGGGTTCCCGGCAGCTGGAGGAACAGCAGAGGCTGAT
CCGGGAGCAGATACACCAGGAGCGTGACCAGTGGTTGAGAGGAAAGACAAAATACTAAAGGCCAAGGAACCCCCAAACTA
AAGCTAAAATGGAAGTGCAAGATGGCTTGGGGGGAGTCAAAAGGTGGCTACTCCAAAGACGTCCTCCTATGGCTTTTGCA
AAAGTATGGTGAGGTTCTCAACATGGTGCTTTCCAGTAAGAAGGTAGGCACTGCTGTGGTGGAGTTTGCGACTGCCAAGG
CTGCAGAGCTGGCTGTCCAGAATGAAGTTGGCCTGGTGGATAACCCTCTGAAGATTTCCTGGTTGGAGGGACAGCCCCAG
AGCACCGTGGGCCCCAGCCGCTCGGCACTGTCAAAGGGCTCAGTGCTGTCGGTGAGGGAATACGAGAGCGTCATCATGAT
GCACATGCGCCACGCGGCCGAGCTGCAATGGCTGATCTCAGAGATGCACCAGCAAGACCGAGAGGGGCAGCCCACG

Alignment

ORF - retro_ptro_1729 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 74.33 %
• Parental protein coverage: 60.86 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  STRTLEQEIERLREEGSRQLEEQQRLIREQIRQERDQRLRGKAENTEGQGTPKLKLK-WKCKKE-DESKG
          STRTLE.EI..L.EEGSRQLEEQQRLIREQI.QERDQ.LRGK.........P..K.K.WKCK....ESKG
Retrocopy STRTLEREIKCLSEEGSRQLEEQQRLIREQIHQERDQWLRGKTKY*RPR-NPQTKAK>WKCKMAWGESKG

Parental  GYSKDVLLRLLQKYGEILNLVLSSKKPGTAVVEFATVKAAELAVQNEVGLVDNPLKISWLEGQPQDAVGR
          GYSKDVLL.LLQKYGE.LN.VLSSKK.GTAVVEFAT.KAAELAVQNEVGLVDNPLKISWLEGQPQ..VG.
Retrocopy GYSKDVLLWLLQKYGEVLNMVLSSKKVGTAVVEFATAKAAELAVQNEVGLVDNPLKISWLEGQPQSTVGP

Parental  SHSGVSKGSVLSERDYESLVMMRMRQAAERQQLIARMQQEDQEGPPT
          S.S..SKGSVLS.R.YES..MM.MR.AAE.Q.LI..M.Q.D.EG.PT
Retrocopy SRSALSKGSVLSVREYESVIMMHMRHAAELQWLISEMHQQDREGQPT

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	8.79 RPM
SRP007412_cerebellum	0.00 RPM	14.41 RPM
SRP007412_heart	0.00 RPM	2.94 RPM
SRP007412_kidney	0.00 RPM	10.62 RPM
SRP007412_liver	0.00 RPM	12.64 RPM
SRP007412_testis	0.11 RPM	2.00 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_1729 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_1729 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_1729 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_2363

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Parental genes homology:

Parental genes homology involve 12 parental genes, and 19 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000020803	4 retrocopies	retro_cjac_1013, retro_cjac_4017, retro_cjac_738, retro_cjac_820,
Cavia porcellus	ENSCPOG00000014110	1 retrocopy	retro_cpor_693,
Homo sapiens	ENSG00000104129	2 retrocopies	retro_hsap_2363, retro_hsap_3468,
Gorilla gorilla	ENSGGOG00000000051	1 retrocopy	retro_ggor_2340,
Macropus eugenii	ENSMEUG00000005641	2 retrocopies	retro_meug_1387, retro_meug_2001,
Myotis lucifugus	ENSMLUG00000014835	1 retrocopy	retro_mluc_317,
Macaca mulatta	ENSMMUG00000013160	1 retrocopy	retro_mmul_1574,
Mus musculus	ENSMUSG00000034278	1 retrocopy	retro_mmus_3346,
Nomascus leucogenys	ENSNLEG00000003257	1 retrocopy	retro_nleu_343,
Pongo abelii	ENSPPYG00000006360	1 retrocopy	retro_pabe_2864,
Pan troglodytes	ENSPTRG00000006929	2 retrocopies	retro_ptro_1729 , retro_ptro_2351,
Rattus norvegicus	ENSRNOG00000012368	2 retrocopies	retro_rnor_18, retro_rnor_2319,