RetrogeneDB ID: retro_ptro_896

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 14:20458358..20459608(+)
• 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_896
GCAGCCTTCGATGATGGGGTGGAAGACGAGTGATCAACGATGAGTACAAAATACGGAAAAAAACACCCCTTTTCTTTACC
ATTTGGTGATGACCCATGCTCTGGAGTGGCCAGCCTAACTGTCCAGTGGCTTCCAGATGAAACCAGACCAGAAGGGAAAG
ATTTCAGCATTCTTCGACTTGTCCTGGGGACACACACATTGGATGAACAAAACCATCTTGTTACAGCCAGCGTGCGACCC
CTAATGATGATGCTCAGTTTGACGCGTCACACTACGACAGTGAGAAAGGAGAATTTGGAGGTTTTGATTCAGTTAGTGGA
AAAATTGAAATAGAAATCAAGATCAACCATGAAGGAGAAGTAAACAGGGCCCGTTATATGCCCCAGAACCCTTGTATCAT
CACAACAAAGACTCCTTCCAGTGATGTTCTTGTCTTTGACTATACAAAACATCCTTCTAAACCAGATCCTTCTGGAGAGT
GCAACCCAGACTTGCGTCTCTGTGGACATCAGAAGGAAGGCTATGGGCTTTCATGGAACCCAAATCTCAGTGGGCATTTA
CTTAGTGCTTCAGATGACCACACTGTCTGCCTGTGGGACAGCAGTGCCATTCCAAAGGAGGGAAAAGTGGATGCAAGGAC
CATCTTTACAGGGCATACAGCAGTAGTAGAAGATGTTTTCTGGCATCTGCTTCATGAGTCTCTGTTTAGGTCAGTTGCTG
ATGATCAGAAACTTATGATTTGGGATACTCGTTCAAAAAATACTTCCAAACCAAGCCACTCAGTTGATGCTTACACTGCT
GAAGTGAACTGCCTCTCTTTCAATCCTTATGGTGAGTTCATTCTTGCTACAGGTTCAGCTGACAAGACTGTTGCCTTGTG
GGATCTGAGAAATCTGAAACTTAAGGTACATTCCTTTGAGTCACATAAGGATGAAATATTCCAGGTTCAGTGGTCACCTC
ACAATGAGACTATTTTGGCTTCCAGTGGTACTGATCGTGGACTGAATATCTGGGATTTAAGTAAAATCGCGGAGGAACAA
TCCCCAGAAGATGCAGAAGACAGGCCACCAGAGTTGTTTATTCATGGTGGTCACATTGCCAAGATACCTGATTTCTCCTG
GAATCCCAGTGAACCTTGGATGATTTGTTCTGTATCAGAAAACAACATCATGGAAGTGTGGCAAATGGCAGAGAACATTT
CTAACGGTGAGGACCCTGAAGGGAGTATGGATCCAGAAGGACAAGAGTCC

Alignment

ORF - retro_ptro_896 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 81.65 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  SVFEDTVEE-RVINEEYKIWKK-NTPFLYDLVMTHALQWP-SLTVQWLPEVTKPEGKDYALHWLVLGTHT
          ..F.D.VE..RVIN.EYKI.KK.NTPFLY.LVMTHAL.WP.SLTVQWLP..T.PEGKD.....LVLGTHT
Retrocopy AAFDDGVED<RVINDEYKIRKK<NTPFLYHLVMTHALEWP<SLTVQWLPDETRPEGKDFSILRLVLGTHT

Parental  SDEQNHLVVARVH-IPNDDAQFDASHCDSDKGEFGGFGSVTGKIECEIKINHEGEVNRARYMPQNPHIIA
          .DEQNHLV.A.V...PNDDAQFDASH.DS.KGEFGGF.SV.GKIE.EIKINHEGEVNRARYMPQNP.II.
Retrocopy LDEQNHLVTASVR<TPNDDAQFDASHYDSEKGEFGGFDSVSGKIEIEIKINHEGEVNRARYMPQNPCIIT

Parental  TKTPSSDVLVFDYTKHPAKPDPSGECNPDLRLRGHQKEGYGLSWNSNLSGHLLSASDDHTVCLWDINAGP
          TKTPSSDVLVFDYTKHP.KPDPSGECNPDLRL.GHQKEGYGLSWN.NLSGHLLSASDDHTVCLWD..A.P
Retrocopy TKTPSSDVLVFDYTKHPSKPDPSGECNPDLRLCGHQKEGYGLSWNPNLSGHLLSASDDHTVCLWDSSAIP

Parental  KEGKIVDAKAIFTGHSAVVEDVAWHLLHESLFGSVADDQKLMIWDTRSNTTSKPSHLVDAHTAEVNCLSF
          KEGK.VDA..IFTGH.AVVEDV.WHLLHESLF.SVADDQKLMIWDTRS..TSKPSH.VDA.TAEVNCLSF
Retrocopy KEGK-VDARTIFTGHTAVVEDVFWHLLHESLFRSVADDQKLMIWDTRSKNTSKPSHSVDAYTAEVNCLSF

Parental  NPYSEFILATGSADKTVALWDLRNLKLKLHTFESHKDEIFQVHWSPHNETILASSGTDRRLNVWDLSKIG
          NPY.EFILATGSADKTVALWDLRNLKLK.H.FESHKDEIFQV.WSPHNETILASSGTDR.LN.WDLSKI.
Retrocopy NPYGEFILATGSADKTVALWDLRNLKLKVHSFESHKDEIFQVQWSPHNETILASSGTDRGLNIWDLSKIA

Parental  EEQSAEDAEDGPPELLFIHGGHTAKISDFSWNPNEPWVICSVSEDNIMQIWQMAENIYNDEESDVTTSEL
          EEQS.EDAED.PPE.LFIHGGH.AKI.DFSWNP.EPW.ICSVSE.NIM..WQMAENI.N.E.........
Retrocopy EEQSPEDAEDRPPE-LFIHGGHIAKIPDFSWNPSEPWMICSVSENNIMEVWQMAENISNGEDPE-GSMDP

Parental  EGQGS
          EGQ.S
Retrocopy EGQES

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	0.80 RPM	36.30 RPM
SRP007412_cerebellum	0.86 RPM	32.34 RPM
SRP007412_heart	0.82 RPM	45.09 RPM
SRP007412_kidney	0.92 RPM	48.41 RPM
SRP007412_liver	0.56 RPM	28.35 RPM
SRP007412_testis	1.90 RPM	63.76 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_896 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_896 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_896 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_1305
Gorilla gorilla	retro_ggor_1022
Pongo abelii	retro_pabe_1093

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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,