RetrogeneDB ID: retro_ptro_2226

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 5:14959171..14960428(-)
• Located in intron of: ENSPTRG00000016739

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_2226
GCAGCCTTCGACAACACAGTGGAAGAATGAGTGATCAACAAGGAATACAAAATATGGAAAAAGAACACCCCTTTTCTTTA
TGATCTGGTGATGACCCATGCTCTGGAGTGGCCCAGCCTAACTGCCCAGTGGCTTCCAGATGTAACCAGACCAGAAGGGA
AAGATTTCAGCCTTCATCGACTTGTCCTGGGGACACACACATCGGATGAACAAAACCATCTTGTTACAGCCAGTGTGCGA
CTCCCTGATGATGATGCTCAGTTTGATGCATCACACTACGACAGTGAGAAATAAGAATTTGGAGGTTTTGGTTCAGTTAG
TGGAAAAATTGAAATAGAAATCAAGATCAACCACGAAGGAAAAGTAAACAGGGCCCGTTATATGCCCCAGAACCCTTGTA
TCATCACAACAAAGACTCCTTCCAGTGATATTCTTGTCTTTGACTATACAAAACATCCTTCTAAACCAGATCCTTCTGGA
GAATGCAACCCAGACTTGCGTCTCCATGGACATCAGAAGGAAGGCTATGGGCTTTCTTGGAACCTAAATCTCAGTGGGCA
CTTACTTAGTGCTTCAGATGACCACACCATCTGCCTGTGGGACATCAGTGCCATTCCAAAGGAGGGAAAAGTGGTAGATG
CAAAGACCATCTTTACAGGGCATACGGCAGTAGTAGAAGATGTTTCCTGGCATCTACTCCGTGAGTCTCTGTTTGGGTCA
GTTGCTGATGATCAGAAACTTATGATTTGGGATACTCGTTCAAACAATACTTCCAAACCAAGCCACTAAGTTGACACTCA
CACTGCTGAAGTGAACTGCCTTTCTTTCAGTCCTTATAGTGAGTTCATTCTTGCCACAGGATCAGCTGACAAGACTGTTG
CCTTGTGGGATCTGAGAAATCTGAAACTTAAGTTGCATTCCTTTGAGTCACATAAGGATGAAATATTCCAGGTTCAGTGG
TCACCTCACAATGAGACTATTTTAGCTTCCAGTGGTACTGATCACAGACTGAATGTCTAGGATTTAAGTAAAATTGGAGA
GGAACAATCTCCAGAAGATGCAGAAGACGGGCCACCAGAGTTGTTTATTCATGGTGGTCACACTGCCAAGATACCTGATT
TCTCCTGGAATCCCAATGAACCTTGGGTGATTTGTTCTGTATCGGAAGACAATATCATGCAAGTGTGGCAAATGGCAGAG
AACATTTATAATGATGAAGACCCTGAAGGAAGCATGGATCCAGAAGGACAAGGGTCC

Alignment

ORF - retro_ptro_2226 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.99 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 4
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  SVFEDTVEERVINEEYKIWKKNTPFLYDLVMTHALQWPSLTVQWLPEVTKPEGKDYALHWLVLGTHTSDE
          ..F..TVEE.VIN.EYKIWKKNTPFLYDLVMTHAL.WPSLT.QWLP.VT.PEGKD..LH.LVLGTHTSDE
Retrocopy AAFDNTVEE*VINKEYKIWKKNTPFLYDLVMTHALEWPSLTAQWLPDVTRPEGKDFSLHRLVLGTHTSDE

Parental  QNHLVVARVHIPNDDAQFDASHCDSDKGEFGGFGSVTGKIECEIKINHEGEVNRARYMPQNPHIIATKTP
          QNHLV.A.V..P.DDAQFDASH.DS.K.EFGGFGSV.GKIE.EIKINHEG.VNRARYMPQNP.II.TKTP
Retrocopy QNHLVTASVRLPDDDAQFDASHYDSEK*EFGGFGSVSGKIEIEIKINHEGKVNRARYMPQNPCIITTKTP

Parental  SSDVLVFDYTKHPAKPDPSGECNPDLRLRGHQKEGYGLSWNSNLSGHLLSASDDHTVCLWDINAGPKEGK
          SSD.LVFDYTKHP.KPDPSGECNPDLRL.GHQKEGYGLSWN.NLSGHLLSASDDHT.CLWDI.A.PKEGK
Retrocopy SSDILVFDYTKHPSKPDPSGECNPDLRLHGHQKEGYGLSWNLNLSGHLLSASDDHTICLWDISAIPKEGK

Parental  IVDAKAIFTGHSAVVEDVAWHLLHESLFGSVADDQKLMIWDTRSNTTSKPSHLVDAHTAEVNCLSFNPYS
          .VDAK.IFTGH.AVVEDV.WHLL.ESLFGSVADDQKLMIWDTRSN.TSKPSH.VD.HTAEVNCLSF.PYS
Retrocopy VVDAKTIFTGHTAVVEDVSWHLLRESLFGSVADDQKLMIWDTRSNNTSKPSH*VDTHTAEVNCLSFSPYS

Parental  EFILATGSADKTVALWDLRNLKLKLHTFESHKDEIFQVHWSPHNETILASSGTDRRLNVWDLSKIGEEQS
          EFILATGSADKTVALWDLRNLKLKLH.FESHKDEIFQV.WSPHNETILASSGTD.RLNV.DLSKIGEEQS
Retrocopy EFILATGSADKTVALWDLRNLKLKLHSFESHKDEIFQVQWSPHNETILASSGTDHRLNV*DLSKIGEEQS

Parental  AEDAEDGPPELLFIHGGHTAKISDFSWNPNEPWVICSVSEDNIMQIWQMAENIYNDEESDVTTSELEGQG
          .EDAEDGPPE.LFIHGGHTAKI.DFSWNPNEPWVICSVSEDNIMQ.WQMAENIYNDE.........EGQG
Retrocopy PEDAEDGPPE-LFIHGGHTAKIPDFSWNPNEPWVICSVSEDNIMQVWQMAENIYNDEDPE-GSMDPEGQG

Parental  S
          S
Retrocopy S

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	2.99 RPM	36.30 RPM
SRP007412_cerebellum	2.83 RPM	32.34 RPM
SRP007412_heart	1.87 RPM	45.09 RPM
SRP007412_kidney	3.79 RPM	48.41 RPM
SRP007412_liver	1.54 RPM	28.35 RPM
SRP007412_testis	9.06 RPM	63.76 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_2226 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_2226 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_2226 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_3292
Gorilla gorilla	retro_ggor_1314
Pongo abelii	retro_pabe_2720

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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,