RetrogeneDB ID: retro_ptro_1802

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 3:99621629..99622269(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RBBP7
• Ensembl ID: ENSPTRG00000021702
• Aliases: None
• Description: retinoblastoma binding protein 7 [Source:HGNC Symbol;Acc:9890]

Sequence

>retro_ptro_1802
TTTGACAACGCAGTGGAAGAACATGTGATCAAGGAGGAGTACAAAATATGGAAAAATAACACCTCTTTTCCTTATGATTT
GGTGATGACGCAGGCTCTGGAGTGGCCCAGCCTAACTGCACAGTGGCTTCCAGATGTAACCAGACCAGAAGGGAAAGATT
TCAGCAGTCATCGACTTGTCCCGGGTACACACACATCAGTTGAACAAAACCACCTTGTGCAGCTTCCTAGTGATGATGCT
CAGCTTGACACATCACACTACAACAGCAAGAAAGGAGAATGTGGAGGTTGAGGTTCGGTTAGTGGAAAAATTGAAAGAGA
AATCAACACCAAGCTGAAGAAGTAAACAGGGCCTGATATATTCCCCAACACCCTTGTAGCATCACAACAAAGACTCCATC
CAGTGATGTTTTTGTCTTTGACTATACAAAACATCCTTCTAAACCAGACCCTATGAAGAGTGAATTCCAGATTTGCATCT
CTGTGGACATCAGAAGGCAGGCTGTGGGCTTTTAAGGAACCCAAATCTTAGTGGACACTTACTTATTACTTCACATAACC
ACACCATCTGCCTATGGGACATCAGTGCTGTTTCAAATGAAGAAAAAGTGTTGGATGTAAAGACCATCTTTACAGGGCAT

Alignment

ORF - retro_ptro_1802 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 65.77 %
• Parental protein coverage: 52.02 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  FEDTVEERVINEEYKIWKKNTPFLYDLVMTHALQWPSLTVQWLPEVTKPEGKDYALHWLVLGTHTSDEQN
          F...VEE.VI.EEYKIWK.NT.F.YDLVMT.AL.WPSLT.QWLP.VT.PEGKD...H.LV.GTHTS.EQN
Retrocopy FDNAVEEHVIKEEYKIWKNNTSFPYDLVMTQALEWPSLTAQWLPDVTRPEGKDFSSHRLVPGTHTSVEQN

Parental  HLVVARVHIPNDDAQFDASHCDSDKGEFGGFGSVTGKIECEIKIN-HEGE-VNRARYMPQNPHIIATKTP
          HL....V..P.DDAQ.D.SH..S.KGE.GG.GSV.GKI..E..IN.H..E.VNRA.Y.PQ.P..I.TKTP
Retrocopy HL----VQLPSDDAQLDTSHYNSKKGECGG*GSVSGKI--EREIN<HQAEEVNRA*YIPQHPCSITTKTP

Parental  SSDVLVFDYTKHPAKPDPSG-ECNPDLRLRGHQKEGYGLSWNSNLSGHLLSASDDHTVCLWDINAGPKEG
          SSDV.VFDYTKHP.KPDP...E..PDL.L.GHQK.G.GL..N.NLSGHLL..S..HT.CLWDI.A...E.
Retrocopy SSDVFVFDYTKHPSKPDPMK<E*IPDLHLCGHQKAGCGLLRNPNLSGHLLITSHNHTICLWDISAVSNEE

Parental  KIVDAKAIFTGH
          K..D.K.IFTGH
Retrocopy KVLDVKTIFTGH

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	36.30 RPM
SRP007412_cerebellum	0.00 RPM	32.34 RPM
SRP007412_heart	0.03 RPM	45.09 RPM
SRP007412_kidney	0.00 RPM	48.41 RPM
SRP007412_liver	0.00 RPM	28.35 RPM
SRP007412_testis	0.00 RPM	63.76 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_1802 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_1802 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_1802 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_2675
Gorilla gorilla	retro_ggor_1867

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Parental genes homology:

Parental genes homology involve 11 parental genes, and 21 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000002820	1 retrocopy	retro_btau_1579,
Mus musculus	ENSMUSG00000031353	1 retrocopy	retro_mmus_3529,
Oryctolagus cuniculus	ENSOCUG00000000683	1 retrocopy	retro_ocun_1939,
Otolemur garnettii	ENSOGAG00000014995	1 retrocopy	retro_ogar_2220,
Petromyzon marinus	ENSPMAG00000007189	1 retrocopy	retro_pmar_26,
Pan troglodytes	ENSPTRG00000001711	1 retrocopy	retro_ptro_1281,
Pan troglodytes	ENSPTRG00000021702	5 retrocopies	retro_ptro_1802 , retro_ptro_1909, retro_ptro_2226, retro_ptro_2987, retro_ptro_896,
Rattus norvegicus	ENSRNOG00000005157	1 retrocopy	retro_rnor_1182,
Sorex araneus	ENSSARG00000008079	3 retrocopies	retro_sara_308, retro_sara_571, retro_sara_602,
Tupaia belangeri	ENSTBEG00000010151	2 retrocopies	retro_tbel_3031, retro_tbel_4341,
Tarsius syrichta	ENSTSYG00000002385	4 retrocopies	retro_tsyr_1608, retro_tsyr_1838, retro_tsyr_1957, retro_tsyr_427,