RetrogeneDB ID: retro_ptro_1909

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 3:97080242..97080977(-)
• Located in intron of: ENSPTRG00000015132

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_1909
ACACACACATTGGATGAACAAAAACATCTTGTTATAGCCAGTGTGCAACTCCCTAATGATGATGCTCATTTTGATGCATC
ACACTATGACAGTGAGAAAGGAGAATTTGGAGGTTTTGGTTCAGTTAGTGGAAAAATTGAAATAGAAATCAAGATCAACC
ATGAAGGAGAAGTAAACAGGGCCCGTTATATGCCCCAGAATCCTTGTATTATCACAACAAAGACTCCTTCCAGTGATGTT
CTTGTCTTGGACTATACAAAACATCCTAAACCAGATCTTTCTGGAGACTGCAACTCAGACTTGCGTCTCCATGGACATCA
GAAAAAAGGCTATGGGCTTTCTTGGCCAAATCTCAGTGGGCACTTACTTAGTGCTTCAGATGATCACACCATCTACCTGT
GGGACATCAGTGCTGTTCCAAAGGAGGGAAATGTGGTGGATGCAAAGACCATCTTTACAGGGCATACAGTAGTAGTAGAA
GATGTTTCCTGGCATCTGTTCCATAAGTCTCTGTTTGGGTCAGTTGCTGATCATCAGAAACTTATGATTTGGGATACTTG
TTCAAACAATACTTCCAAACCAAGCCACTCAGTTGACGCTCACACTGCTGAAGTGAACTGCCTCTCTTTCAATCCTTATA
GTGAGTTCATTCTTGCCACAGGATCAGCTGACAAGACTGTTGCCTTGTGGGATCTGAGAAATCTGAAACTTATGTTGCAT
TCCTCTGAGTCACAT

Alignment

ORF - retro_ptro_1909 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 83.4 %
• Parental protein coverage: 58.67 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  THTSDEQNHLVVARVHIPNDDAQFDASHCDSDKGEFGGFGSVTGKIECEIKINHEGEVNRARYMPQNPHI
          THT.DEQ.HLV.A.V..PNDDA.FDASH.DS.KGEFGGFGSV.GKIE.EIKINHEGEVNRARYMPQNP.I
Retrocopy THTLDEQKHLVIASVQLPNDDAHFDASHYDSEKGEFGGFGSVSGKIEIEIKINHEGEVNRARYMPQNPCI

Parental  IATKTPSSDVLVFDYTKHPAKPDPSGECNPDLRLRGHQKEGYGLSWNSNLSGHLLSASDDHTVCLWDINA
          I.TKTPSSDVLV.DYTKHP.KPD.SG.CN.DLRL.GHQK.GYGLSW..NLSGHLLSASDDHT..LWDI.A
Retrocopy ITTKTPSSDVLVLDYTKHP-KPDLSGDCNSDLRLHGHQKKGYGLSW-PNLSGHLLSASDDHTIYLWDISA

Parental  GPKEGKIVDAKAIFTGHSAVVEDVAWHLLHESLFGSVADDQKLMIWDTRSNTTSKPSHLVDAHTAEVNCL
          .PKEG..VDAK.IFTGH..VVEDV.WHL.H.SLFGSVAD.QKLMIWDT.SN.TSKPSH.VDAHTAEVNCL
Retrocopy VPKEGNVVDAKTIFTGHTVVVEDVSWHLFHKSLFGSVADHQKLMIWDTCSNNTSKPSHSVDAHTAEVNCL

Parental  SFNPYSEFILATGSADKTVALWDLRNLKLKLHTFESH
          SFNPYSEFILATGSADKTVALWDLRNLKL.LH..ESH
Retrocopy SFNPYSEFILATGSADKTVALWDLRNLKLMLHSSESH

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	0.38 RPM	36.30 RPM
SRP007412_cerebellum	0.43 RPM	32.34 RPM
SRP007412_heart	0.26 RPM	45.09 RPM
SRP007412_kidney	0.37 RPM	48.41 RPM
SRP007412_liver	0.07 RPM	28.35 RPM
SRP007412_testis	0.53 RPM	63.76 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_1909 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_1909 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_1909 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_2814

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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,