RetrogeneDB ID: retro_ptro_2987

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: GL390389.1:1082577..1083387(-)
• 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_2987
GCAGCCTTTGACGACGCAGTGGAAGAACGAGGGATCAACAAGGAGTACAAAAAATGGAAAAAGAACACCCCTTTTCTTTA
TGATTTAGTGTTGACCCATGCTCTGGAGTGGCCCAGCCTAACTGCCCAGTGGCTTCCAGATATAACCAGACCAGAAGGGA
AAGATTTCAGCATTCATCAACTTGTCCTGGGGACATACACATTGGATGAACAAAACCATCTCATTATAGCCAGTGTGCAA
CTCCCTAATGATGACGCTCAGTTTGATGCGTCACACTACAACACTGAGAAAGGAGAATTTGGAGGTTTTTATTCAGTTAG
AGGAAAAATTGAAATAGAAATCAAGATCAACCATGAAGGAGAAGTAAACAAGGTCCATTATATGCCCCAGAACCCTTGTA
TCATCTCAACTAAGACTCCTTCCAGTGATGTTCTTGTCTTTGACTATACAAAACACCTTTCTAAACCAGATCCTTCTGGA
GAGTGCGATCCAGACTTGTGTCTCCGTGGACATCAGAAGGAAGGCTATGGGCTTTCTTGGAACCCAAATCTCTGTGGGCA
CTTACTTAGTGCTTCAGATGACCACACCAGCTGCCTGTGGGACATCAGTGCTGTTCCAAAGGAGAGAAAAGTGGTGGATG
TGAAGACCATCTTTACAGGGCATACAGCAGTAGTAGATGTTTCCTGGCATCTGCTCCATGAGTCTCTGTTTGGGTCAGTT
GCTGATGATCAGAAACTTATGATTTGGGATACTTGTTCAAACAGTGCTTCCAAACCAAGCCGTTCAGTTGACGCTCACAC
TGCTGAAGTG

Alignment

ORF - retro_ptro_2987 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 78.97 %
• Parental protein coverage: 64.37 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  SVFEDTVEERVINEEYKIWKKNTPFLYDLVMTHALQWPSLTVQWLPEVTKPEGKDYALHWLVLGTHTSDE
          ..F.D.VEER.IN.EYK.WKKNTPFLYDLV.THAL.WPSLT.QWLP..T.PEGKD...H.LVLGT.T.DE
Retrocopy AAFDDAVEERGINKEYKKWKKNTPFLYDLVLTHALEWPSLTAQWLPDITRPEGKDFSIHQLVLGTYTLDE

Parental  QNHLVVARVHIPNDDAQFDASHCDSDKGEFGGFGSVTGKIECEIKINHEGEVNRARYMPQNPHIIATKTP
          QNHL..A.V..PNDDAQFDASH....KGEFGGF.SV.GKIE.EIKINHEGEVN...YMPQNP.II.TKTP
Retrocopy QNHLIIASVQLPNDDAQFDASHYNTEKGEFGGFYSVRGKIEIEIKINHEGEVNKVHYMPQNPCIISTKTP

Parental  SSDVLVFDYTKHPAKPDPSGECNPDLRLRGHQKEGYGLSWNSNLSGHLLSASDDHTVCLWDINAGPKEGK
          SSDVLVFDYTKH..KPDPSGEC.PDL.LRGHQKEGYGLSWN.NL.GHLLSASDDHT.CLWDI.A.PKE.K
Retrocopy SSDVLVFDYTKHLSKPDPSGECDPDLCLRGHQKEGYGLSWNPNLCGHLLSASDDHTSCLWDISAVPKERK

Parental  IVDAKAIFTGHSAVVEDVAWHLLHESLFGSVADDQKLMIWDTRSNTTSKPSHLVDAHTAEV
          .VD.K.IFTGH.AVV.DV.WHLLHESLFGSVADDQKLMIWDT.SN..SKPS..VDAHTAEV
Retrocopy VVDVKTIFTGHTAVV-DVSWHLLHESLFGSVADDQKLMIWDTCSNSASKPSRSVDAHTAEV

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	0.09 RPM	36.30 RPM
SRP007412_cerebellum	0.04 RPM	32.34 RPM
SRP007412_heart	0.00 RPM	45.09 RPM
SRP007412_kidney	0.03 RPM	48.41 RPM
SRP007412_liver	0.03 RPM	28.35 RPM
SRP007412_testis	0.42 RPM	63.76 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_2987 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_2987 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_2987 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_3601
Homo sapiens	retro_hsap_3600

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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,