RetrogeneDB ID: retro_ptro_2434

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 6:57209074..57210348(-)
• 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_2434
AAACTTAAAGGGTCAAAGTGCAATGGGCAGCTTTTGATTTTGGGGGCAACTAACTGGGACATGATTGGTCGAAAAGAAGT
GCCTAAACAGCAAGCTGCTTACCGCAATCTCGGTCAGAATTTGTGGGGTCCCCACAGGTATGGCTGTCTGGCGGGGGTCC
GGATACGGACAGTGGTCTCAGGTTCCTGTGCTGCACACAGCCTCCTCATCACCATGGAAGGGAAGCTGTGGAGTTGGGGT
CGAAATGAGAAGGGGCAGCTGGGACTTGGCGACACCAAGAGAGTAGAGGCCCCCAGACTCATCGAGGGTCTCTGCCATGA
AGTGACCATGTCTGCAGCATGTGGGTGGAACCACACCTTGGCCTTGACGAAAACAGGCCCTGTGTTTGCGTTTGGGGAGA
ACAAGATGGGGCAGCTGGGCCTTGCCAACCAGACAGACGCTGTGCAGCCCCGCGCAGATAATGTATAACGGCCAGCCAAT
TACCAAAATGGCCTGTGGGGCTGAATTCAGTATGATAATGGACTGAAAAGGAAACCTCTGTTCCTTTGGGTGCCCTGAAT
ATGGTCAGCTGGGACACAACTCGGATGGGAAGTTCATCTTTGGGGCACAGCGGATAGAGTACGACTGCGAACTGGTTCCC
CCGCAACTGGCCATATTCATTGAGAAGACGAAAGACGGACAGATTCTGCCTGTACCAAACGTGGTTGTGTGAGACGTGGC
CTGTGGTGCTAACCACACGTGGTCCTGGACTCCCAGGAGCGAGTCTTCTCCTGGGGCTTCGGTGGCTATGGCCGGCTCGG
CCACGCAGAGCAGAAGGACGAGATGGTCCGCCGCCTGGTGAAGCTGTTTGACTTCCCTTGGCGTGGTGCGTCCCAGATCT
ATGCTGGTTACACCTGCTCCTTGGCCGTCAGTGAAGTGGGTGGTCTGTTTTTCCGGAGGGCCACCACCATCTCCCGTGAA
TCTGCCATGTACCCGAAAGCAGTGCAGGACCTCTGTGGCTGGAGAATCCAGAGCCTGGCTTGCGGGAAGAGCAGTATCAT
TGTGGCCGCTGACGAGAGCGCCATCAGCTGGGGCCCATCACCGACCTTCGGGGAACTGGGCTAGGGGGACCACAAGCCCA
AGTCTTCCACTGCAGCCCAGGAGGTGAAGACTCTGCATCCACAGTCTTCATTTTCTCAGAGAAGGTCGCCATGGGCTACT
CACACTCCTTGGTGATAGCAAGAGACGAAAGTGAGACCGAGAAAGAGATCAAGAAACTGCCAGAATACAACCCC

Alignment

ORF - retro_ptro_2434 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 81.35 %
• Parental protein coverage: 99.3 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  KLEGSKCKGQLLIFGATNWDLIGRKEVPKQQAAYRNLGQNLWGPHRYGCLAGVRVRTVVSGSCAAHSLLI
          KL.GSKC.GQLLI.GATNWD.IGRKEVPKQQAAYRNLGQNLWGPHRYGCLAGVR.RTVVSGSCAAHSLLI
Retrocopy KLKGSKCNGQLLILGATNWDMIGRKEVPKQQAAYRNLGQNLWGPHRYGCLAGVRIRTVVSGSCAAHSLLI

Parental  TTEGKLWSWGRNEKGQLGHGDTKRVEAPRLIEGLSHEVIVSAACGRNHTLALTETGSVFAF-GENKMGQL
          T.EGKLWSWGRNEKGQLG.GDTKRVEAPRLIEGL.HEV..SAACG.NHTLALT.TG.VFAF.G....G..
Retrocopy TMEGKLWSWGRNEKGQLGLGDTKRVEAPRLIEGLCHEVTMSAACGWNHTLALTKTGPVFAF>GRTRWGSW

Parental  GLGNQTDAVPSPAQIMYNGQPITKMACGAEFSMIMDCKGNLYSFGCPEYGQLGHNSDGKFIARAQRIEYD
          .L........SPAQIMYNGQPITKMACGAEFSMIMD.KGNL.SFGCPEYGQLGHNSDGKFI..AQRIEYD
Retrocopy ALPTR-QTLCSPAQIMYNGQPITKMACGAEFSMIMD*KGNLCSFGCPEYGQLGHNSDGKFIFGAQRIEYD

Parental  CELVPRRVAIFIEKTKDGQILPVPNVVVRDVACGANHT-LVLDSQKRVFSWGFGGYGRLGHAEQKDEMVP
          CELVP...AIFIEKTKDGQILPVPNVVV.DVACGANHT..VLDSQ.RVFSWGFGGYGRLGHAEQKDEMV.
Retrocopy CELVPPQLAIFIEKTKDGQILPVPNVVV*DVACGANHT<VVLDSQERVFSWGFGGYGRLGHAEQKDEMVR

Parental  RLVKLFDFPGRGASQIYAGYTCSFAVSEVGGLFFWGATNTSRESTMYPKAVQDLCGWRIRSLACGKSSII
          RLVKLFDFP.RGASQIYAGYTCS.AVSEVGGLFF..AT..SRES.MYPKAVQDLCGWRI.SLACGKSSII
Retrocopy RLVKLFDFPWRGASQIYAGYTCSLAVSEVGGLFFRRATTISRESAMYPKAVQDLCGWRIQSLACGKSSII

Parental  VAADESTISWGPSPTFGELGYGDHKPKSSTAAQEVKTL--DGIFSEQVAMGYSHS-LVIARDESETEKEK
          VAADES.ISWGPSPTFGELG.GDHKPKSSTAAQEVKTL.....FS........H................
Retrocopy VAADESAISWGPSPTFGELG*GDHKPKSSTAAQEVKTLHPQSSFSQRRSPWATHT<SLVIARDESETEKE

Parental  IKKLPEYNP
          IKKLPEYNP
Retrocopy IKKLPEYNP

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	0.04 RPM	42.93 RPM
SRP007412_cerebellum	0.07 RPM	36.67 RPM
SRP007412_heart	0.03 RPM	11.08 RPM
SRP007412_kidney	0.05 RPM	37.42 RPM
SRP007412_liver	0.03 RPM	32.90 RPM
SRP007412_testis	0.32 RPM	30.46 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_2434 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_2434 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_2434 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_3597
Pongo abelii	retro_pabe_2957

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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,