RetrogeneDB ID: retro_pabe_2547

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 4:113426069..113427103(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RCC2
• Ensembl ID: ENSPPYG00000025834
• Aliases: None
• Description: regulator of chromosome condensation 2 [Source:HGNC Symbol;Acc:30297]

Sequence

>retro_pabe_2547
AAGAAGGGGCAGCTGGGACACAGGGACACCAAGAGAGTGGAAGCCCCCAGACTCATTGAGGGTCTCAGCCACAAAGTGAT
CGTATCTGCAGCATGTGGGCAGAACCACACCTTGGCCTTGAGGGAAACCGGCTCTGTGTTTGCATTTGGGGAGAACAAGA
TGGGGCAGCTGGGCCTTGGCAACCAGACAGACACTATCCACAGCCCCACGCAGATAATGTACAATGGCCAGCCAATTACC
AAAATGACCTGTGAGGGCTGAATTCAGTATGGTAATAGACTGCAGAGGAAACCTCTGTTCCTTTGGGTGCCCTGAATATG
ATCAGCTGGGACACAACTCGGATGGGTAGTTCATTGCCTGGCCAAAGCAGATAGAATACGACTGCAAACTGGTGCCCCAG
CAAGTGGCCATCTTCATCAAGAAGACCAAAAATTGACAGATGCCACCTGTACCAAACGTGGTTGTGCAAGACGTGGCCAG
TGGCGCTAACCACACGCTGGTTCTGGACTCCCAGAAGCAAGTCGTCTTTGGGGCTCCGGTGGCTATGGCTGGTTGGGCCA
TGCAGAGCAGAAGGATGAGATGGTCCCCTGCCTGGTGAAGCTGTTTGACTTTTCTGGAAGTGGGGTGTCCCAGATCTATG
CTGGTTACACCTGCTTCTTTGCCATCAGTGAAGTGGGTGGTCTGTTTTTCTGGGGGTCACCAACACCTCCCATGAATCTA
CCATGTACCCGAAAGCAGTACAGGACCTCTGTGGCTGGAGAATCCAGAGCCTTGCTTGTGGGAAGAGCAGCATCACTGTG
GCCACCAGTGAGAGCACCATCAGCTGGGGCCCATTGCCGACCTTCAGGGAACAGGGCTACAGGGACCACAAGCCCAAGTC
TTCCACTGCAGCCCAAGAGGTGAAGACTCTGGATAGCATTTTCTCAGAGCAGTTCGCCAAGGGCTACTCACACACCTTGG
TGATAGTAAGAGACAAACGCTAGACCGAGAAAGAGAAGATCAAGAAACTGCCAGAATACAACCCCCCAACCCTC

Alignment

ORF - retro_pabe_2547 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 81.61 %
• Parental protein coverage: 66.09 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  EKGQLGHGDTKRVEAPRLIEGLSHEVIVSAACGRNHTLALTETGSVFAFGENKMGQLGLGNQTDAVPSPA
          .KGQLGH.DTKRVEAPRLIEGLSH.VIVSAACG.NHTLAL.ETGSVFAFGENKMGQLGLGNQTD...SP.
Retrocopy KKGQLGHRDTKRVEAPRLIEGLSHKVIVSAACGQNHTLALRETGSVFAFGENKMGQLGLGNQTDTIHSPT

Parental  QIMYNGQPITKMACG-AEFSMIMDCKGNLYSFGCPEYGQLGHNSDGKFIARAQRIEYDCELVPRRVAIFI
          QIMYNGQPITKM.C..AEFSM..DC.GNL.SFGCPEY.QLGHNSDG.FIA....IEYDC.LVP..VAIFI
Retrocopy QIMYNGQPITKMTCE>AEFSMVIDCRGNLCSFGCPEYDQLGHNSDG*FIAWPKQIEYDCKLVPQQVAIFI

Parental  EKTKDGQILPVPNVVVRDVACGANHTLVLDSQKRVFS-WGFGGYGRLGHAEQKDEMVPRLVKLFDFPGRG
          .KTK..Q..PVPNVVV.DVA.GANHTLVLDSQK.V...WG.GGYG.LGHAEQKDEMVP.LVKLFDF.G.G
Retrocopy KKTKN*QMPPVPNVVVQDVASGANHTLVLDSQKQVVF<WGSGGYGWLGHAEQKDEMVPCLVKLFDFSGSG

Parental  ASQIYAGYTCSFAVSEVGGLFFWGA-TNTSRESTMYPKAVQDLCGWRIRSLACGKSSIIVAADESTISWG
          .SQIYAGYTC.FA.SEVGGLFFWG..TNTS.ESTMYPKAVQDLCGWRI.SLACGKSSI.VA..ESTISWG
Retrocopy VSQIYAGYTCFFAISEVGGLFFWGS<TNTSHESTMYPKAVQDLCGWRIQSLACGKSSITVATSESTISWG

Parental  PSPTFGELGYGDHKPKSSTAAQEVKTLDGIFSEQVAMGYSHSLVIARDESETEKEKIKKLPEYNPRTL
          P.PTF.E.GY.DHKPKSSTAAQEVKTLD.IFSEQ.A.GYSH.LVI.RD...TEKEKIKKLPEYNP.TL
Retrocopy PLPTFREQGYRDHKPKSSTAAQEVKTLDSIFSEQFAKGYSHTLVIVRDKR*TEKEKIKKLPEYNPPTL

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	44.01 RPM
SRP007412_cerebellum	0.00 RPM	27.97 RPM
SRP007412_heart	0.00 RPM	8.79 RPM
SRP007412_kidney	0.00 RPM	40.17 RPM
SRP007412_liver	0.00 RPM	14.99 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_2547 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_2547 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_2547 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_3073
Pan troglodytes	retro_ptro_2072
Gorilla gorilla	retro_ggor_2112

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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,