RetrogeneDB ID: retro_tbel_4341

Retrocopy location

• Organism: Treeshrew (Tupaia belangeri)
• Coordinates: scaffold_77665:3382..4208(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RBBP7
• Ensembl ID: ENSTBEG00000010151
• Aliases: None
• Description: retinoblastoma binding protein 7 [Source:HGNC Symbol;Acc:9890]

Sequence

>retro_tbel_4341
TTTGACTATCCAGTGGAAAAACATGTGATCAATGAGGAGTATAAAATATGGAAAAAGAACACTCCTTTTCTTTATGATTT
GGTGATGACCCATGCTCTGGAGTGGCCCTGCCCAACTGCTCAGTGGCTTCCAGATGTAGCCAGATCTGAAGGGAAAGATT
TCAGCATTAATCCACATGTCCTGGGGACACACACCTTGGATAAACAAAACCACCTGGTGTTAGCCAGCGTGCAGCTCCCT
AACTATGATGCTCAGTTTGATTCATCACATTATGACAGTGAAAAAGGAGAATTTGGAGGTTTTGGCTCAGTTAGTGGAAA
AATTGAAATAGAAATTAAGATCAACCATGAAGGAGAAGTAAACAGGGCCCGCTATGTGCCCCAGGACCCTTGTATCATTG
CAACAAAGACTCCATCCAGTGATGTGCTTGTTTTTGACTATAGAAAACATCCTTCTAAGCCAGACTCTTCTGTAGAGTGC
AGCCCAGATTTGTGTCTTTTTGGGACACCAGTAGGAGGGCTATGGGCTTTCTTGGATCCCAAATCTCAGTGGGCACTTAG
TGCTCCCAATGACTATACCATCTGCCTGTGGGACTTCAGTGCTGTTCCAAAGGAAGGAAAAGGGGTGGATACAAAGGCCA
TCTTTTACAGTGCATACAGCAGTAGTGGTAGATGTTTTCCTGGCATCTTCTTTGCTCCATGTATCTCTCTTTGGATCAGT
TTGCTGACGATCAGAAAACTTTGTGATTTGGGGAAACTTCGTCAAAACAATACTTCCCAAAACCAAGGGCATCAGTTTGA
AGCTCACAACTGGAAAAGGAAACTGC

Alignment

ORF - retro_tbel_4341 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 65.23 %
• Parental protein coverage: 57.78 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  FEDTVEERVINEEYKIWKKNTPFLYDLVMTHALQWPSLTVQWLPEVTKSEGKDYAFHWLVLGTHTSDEQI
          F...VE..VINEEYKIWKKNTPFLYDLVMTHAL.WP..T.QWLP.V..SEGKD......VLGTHT.D.Q.
Retrocopy FDYPVEKHVINEEYKIWKKNTPFLYDLVMTHALEWPCPTAQWLPDVARSEGKDFSINPHVLGTHTLDKQN

Parental  HLVVARVHNPNDDAQFDASHCDSDKGEFGGFGSVTGKIECEIKINHEGEVNRARYMPQNPHIIATKTPSS
          HLV.A.V..PN.DAQFD.SH.DS.KGEFGGFGSV.GKIE.EIKINHEGEVNRARY.PQ.P.IIATKTPSS
Retrocopy HLVLASVQLPNYDAQFDSSHYDSEKGEFGGFGSVSGKIEIEIKINHEGEVNRARYVPQDPCIIATKTPSS

Parental  DVLVFDYTKHPAKPDPSGECNPDLRL-RGHQKEGYGLSWNSNLSGHLLSASDDHTVCLWDINAGPKEGKI
          DVLVFDY.KHP.KPD.S.EC.PDL.L..GHQ.EGYGLSW..NLSGHL.........C........KE...
Retrocopy DVLVFDYRKHPSKPDSSVECSPDLCL>LGHQ*EGYGLSWIPNLSGHLVLPMTIPSACGTSVLFQRKEKGW

Parental  VDAKAIFTGHSAVVEDV--AWHLLHESLFGSV-ADDQKLM-IWDTGS-NTTSR-QGHLGE-LSTGEVNC
          ......FT.H.AVV.DV..A..LLH.SLFGSV.ADDQK......T.S.N.TS..QGH..E.L.TG..NC
Retrocopy IQ-RPSFTVHTAVVVDVFLASSLLHVSLFGSV>ADDQKTL*FGETSS>NNTSQNQGHQFE>LTTGKGNC

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Tupaia belangeri was not studied using RNA-Seq expression data.

ChIP-Seq

Tupaia belangeri was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_tbel_4341 retrocopy.

TSS

Tupaia belangeri was not studied using FANTOM5 data.

Lab

retro_tbel_4341 was not experimentally validated.

Homology

Retrocopy orthology:

Tupaia belangeri does not belong to any of the species groups (eutheria, teleost or neognath), studied for retrocopy-based homology. For more information about studied groups, please go to help section.

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Parental genes homology:

Parental genes homology involve 11 parental genes, and 23 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	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	ENSTBEG00000002236	3 retrocopies	retro_tbel_1360, retro_tbel_1718, retro_tbel_3802,
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,