RetrogeneDB ID: retro_ptro_1804

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 3:99813871..99814574(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RCC2
• Ensembl ID: ENSPTRG00000000247
• Aliases: None
• Description: Regulator of chromosome condensation 2 [Source:UniProtKB/TrEMBL;Acc:K7ABL4]

Sequence

>retro_ptro_1804
AAACTTGAAGGGTCGAAGTACAATGGGCAACTTTTGATTTGAAGGGCAGTCAACTGGGACTTGACTGGTTGAAAGGAAGT
ACCTAAACAGCAAAAGCTGCTTACGGCAATCTCGGTCAGAATTTGTGAGGGGCCTCAGATATGTGGGTACCTGGTAGCGC
CCAGGTGTGGGCAGTGGTTTCTGGTTAGTGTGCTGCTCACAGCCTCCTCATCACCATAGAAGAGAAGCTGTGGAGCTGCT
GTGGACAAGAGAAGGGGCATCTGGGACATGACAACACCAAGAGAGTGGAAGCTCCCAGACTCATCAAAGGTCTTAGCCAT
GAAGTGATCCTGCCGTCAGCATGTGGGCAGAACCACACACTGACCTTGACAGAAACCAGCTCCTTGTTCACATTTGGGGA
GAACAAGATGGCATAGCTGGGCCGTGGTAACCAGACAGATGCTGTCCACACCTTGGCACAGACAAGGTATAAAGGCCAGC
CCATTACCAAAATGACCTGTGGAGTTGAATTCAGCGTGATAATGGACTGCAAAGGAAACCCCTTTTCCTTTGGGTGCCCT
GAATATGGTCAGCTGGGACACAATTGGATGGGAAGTTCATCATCCCGATGCAGCCATTAGAATATTACTGAAAACTGGTG
CTCCTGCAATTGGCTGTCTTCATCCAGAAAACAGAAGATGGACAGATTCTGCCTGTACCAAAT

Alignment

ORF - retro_ptro_1804 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 66.67 %
• Parental protein coverage: 54.8 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  KLEGSKCKGQLLIFGATNWDLIGRKEVPKQQAAYRNLGQNLW-GPHRYGCLAGVR-VRTVVSGSCAAHSL
          KLEGSK..GQLLI..A.NWDL.G.KEVPKQQ............GP...G.L...R.V..VVSG.CAAHSL
Retrocopy KLEGSKYNGQLLI*RAVNWDLTG*KEVPKQQKLLTAISVRICEGPQICGYLVAPR<VWAVVSG*CAAHSL

Parental  LITTEGKLWSWGRNEKGQLGHGDTKRVEAPRLIEGLSHEVIVSAACGRNHTLALTETGSVFAFGENKMGQ
          LIT.E.KLWS....EKG.LGH..TKRVEAPRLI.GLSHEVI...ACG.NHTL.LTET.S.F.FGENKM..
Retrocopy LITIEEKLWSCCGQEKGHLGHDNTKRVEAPRLIKGLSHEVILPSACGQNHTLTLTETSSLFTFGENKMA*

Parental  LGLGNQTDAVPSPAQIMYNGQPITKMACGAEFSMIMDCKGNLYSFGCPEYGQLGHN-SDGKFIARAQRIE
          LG.GNQTDAV...AQ..Y.GQPITKM.CG.EFS.IMDCKGN..SFGCPEYGQLGHN..DGKFI...Q..E
Retrocopy LGRGNQTDAVHTLAQTRYKGQPITKMTCGVEFSVIMDCKGNPFSFGCPEYGQLGHN<LDGKFIIPMQPLE

Parental  YDCELVPRRVAIFIEKTKDGQILPVPN
          Y...LV....A.FI.KT.DGQILPVPN
Retrocopy YY*KLVLLQLAVFIQKTEDGQILPVPN

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	42.93 RPM
SRP007412_cerebellum	0.00 RPM	36.67 RPM
SRP007412_heart	0.00 RPM	11.08 RPM
SRP007412_kidney	0.00 RPM	37.42 RPM
SRP007412_liver	0.00 RPM	32.90 RPM
SRP007412_testis	0.00 RPM	30.46 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_1804 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_1804 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_1804 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_2677

---

Parental genes homology:

Parental genes homology involve 8 parental genes, and 15 retrocopies.

Species	Parental gene accession	Retrocopies number
Dasypus novemcinctus	ENSDNOG00000001396	1 retrocopy	retro_dnov_2692,
Homo sapiens	ENSG00000179051	3 retrocopies	retro_hsap_2677, retro_hsap_3073, retro_hsap_3597,
Gorilla gorilla	ENSGGOG00000015263	1 retrocopy	retro_ggor_2112,
Nomascus leucogenys	ENSNLEG00000007783	2 retrocopies	retro_nleu_2483, retro_nleu_298,
Otolemur garnettii	ENSOGAG00000014544	1 retrocopy	retro_ogar_2967,
Pongo abelii	ENSPPYG00000025834	3 retrocopies	retro_pabe_2547, retro_pabe_2957, retro_pabe_748,
Pan troglodytes	ENSPTRG00000000247	3 retrocopies	retro_ptro_1804 , retro_ptro_2072, retro_ptro_2434,
Rattus norvegicus	ENSRNOG00000006327	1 retrocopy	retro_rnor_1378,