RetrogeneDB ID: retro_sara_571

Retrocopy location

• Organism: Shrew (Sorex araneus)
• Coordinates: scaffold_234922:680..1936(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RBBP7
• Ensembl ID: ENSSARG00000008079
• Aliases: None
• Description: retinoblastoma binding protein 7 [Source:HGNC Symbol;Acc:9890]

Sequence

>retro_sara_571
AGAGTGAGAGCGCTCGCAGCCTCCCTGCCCCTTCCGCAAAGCTCGACTAGGGGAATCTCTGCAGCTCGCCTGCCCATGGC
CGACGAGGAAGCAGCCTTTAATGACACAGTCGAAGAACGTGTGATCAATGAAGAGTACAAAATATGGAAGAACAATACCC
CTTTTCTTTACGATTTGGTGATGACCCATGCTCTGGAGTGGCCCAGCCTCACTGCACAGTGGCTTCCAGATGTGACCAGA
CCAGAAGGAAAAGATTTCAGCATTCATTGACTTGTTCTGGGGGACAACACACATCAGATGAACAAAACCACCTTGTGATA
GCCAGTTTGCAGTTCCCTAATGATGATGCCCAGTTTTGATGCTTTCACACTATGACAGTGAGAAAGGAGAATTTGGAGGT
TTTGGCTCAGTTAATGGAAAAATTGAGATAGAGATCAAGATCAACCATGGAGGAGAAGTAAACAGGGCACGTTACATGCC
TCAGAACTCTTGCATCATTGCAACAAAAACTCCATCCAGTGATGTTCTTGTTTTTGACTATACAAAGCATCCTTCGAAAC
CAGACCCTTCTGGTGAGTGCAACCCAGACTTGCATCTCCCGGGACATCAGAAGGAAGGATATGGGCTTTCTTGGAACCCA
AATCTCAGTGGGCACTTACTTAGTGCTTCCGATGACCATACCATCTGCCTGTGGGACATCAGTGCTGTTCCAAAGGAAGG
AAAAATTGTGGATGCCAAGACCATCTTTACAGGCCACACAGCAGTAGAGAGGATGTTTCCTGGCATCTGCTCCATGAGTC
TTTGTTGGTTCAGTTGCCAATGATCAGAAACTTATGATTTGGGATACTCATTCAAACAATACTTCCAAACCAAGCCACTC
AGTTGATGCTCACATTGCTGAAGTGAACTGCCTGTCTTTCAACCCTTACAGTGAGTTCATTCTTGCCACAGGATCGGCTG
ACAAGACTGTTGGCTTGTGGGATCTGAGAAATCTGAAACTTAAGTTGCATTCCTTTGAATCACACAAGGATAAAATATTC
CAGGTTCAGTGGTCACCTCACAATGAGACTATTTTGGCTTCCAGTGGAACTGATCGTAGACTGAATGTTTGGGAACTTGA
GTAAAATTGGAGAAGAACAATCCCCAGAAGATGCAGAGGATGGGCCACCAGAATTACTGTTTATCCATGGTGGTCACACT
GCCAAAATACCTGATTTCTCTTGGAATCCAATGAGCTTTAGGTGATTTGTTCATTA

Alignment

ORF - retro_sara_571 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 74.65 %
• Parental protein coverage: 89.27 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 7

Retrocopy - Parental Gene Alignment:

Parental  RERAVGFLLHVDSPPGVGRGALLLPGRHFGTVFEDTVEERVINEEYKIWKKNTPFLYDLVMTHALQWPSL
          R.RA....L........G..A..LP.......F.DTVEERVINEEYKIWK.NTPFLYDLVMTHAL.WPSL
Retrocopy RVRALAASLPLPQSSTRGISAARLPMADEEAAFNDTVEERVINEEYKIWKNNTPFLYDLVMTHALEWPSL

Parental  TVQWLPEVTKPEGKDYALHWLVLGTHT-SDEQNHLVV-ARVHIPNDDAQ-FDA-SHCESDKGEFGGFGSV
          T.QWLP.VT.PEGKD...H.LVLG..T.........V.A....PNDDAQ.FDA.SH..S.KGEFGGFGSV
Retrocopy TAQWLPDVTRPEGKDFSIH*LVLGDNT<TSDEQNHLVIASLQFPNDDAQ>FDA>SHYDSEKGEFGGFGSV

Parental  TGKIECEIKINHEGEVNRARYMPQNPHIIATKTPSSDVLVFDYTKHPAKPDPSGECNPDLRLRGHQKEGY
          .GKIE.EIKINH.GEVNRARYMPQN..IIATKTPSSDVLVFDYTKHP.KPDPSGECNPDL.L.GHQKEGY
Retrocopy NGKIEIEIKINHGGEVNRARYMPQNSCIIATKTPSSDVLVFDYTKHPSKPDPSGECNPDLHLPGHQKEGY

Parental  GLSWNSNLSGHLLSASDDHT--RLDINAGPKEGKIVDAKGIFTGHSAVV-EDVAWHLLHESLF-GSVADD
          GLSWN.NLSGHLLSASDDHT....DI.A.PKEGKIVDAK.IFTGH.AV..EDV.WHLLHESL..GSVA.D
Retrocopy GLSWNPNLSGHLLSASDDHTICLWDISAVPKEGKIVDAKTIFTGHTAVE<EDVSWHLLHESLL<GSVAND

Parental  QKLMIWDTRSNTTSKPSHLVDAHTAEVNCLSFNPYSEFILATGSADKTVALWDLRNLKLKLHTFESHKDE
          QKLMIWDT.SN.TSKPSH.VDAH.AEVNCLSFNPYSEFILATGSADKTV.LWDLRNLKLKLH.FESHKD.
Retrocopy QKLMIWDTHSNNTSKPSHSVDAHIAEVNCLSFNPYSEFILATGSADKTVGLWDLRNLKLKLHSFESHKDK

Parental  IFQVHWSPHNETILASSGTDRRLNVWD-LSKIGEEQSAEDAEDGPPELLXXXXXXXXXXXDISRIPY-EC
          IFQV.WSPHNETILASSGTDRRLNVW..LSKIGEEQS.EDAEDGPPELL...........D.S..P..E.
Retrocopy IFQVQWSPHNETILASSGTDRRLNVWE>LSKIGEEQSPEDAEDGPPELLFIHGGHTAKIPDFSWNPM<EL

Parental  GIICSL
          ..ICSL
Retrocopy *VICSL

Legend:

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

Expression

RNA-Seq

Sorex araneus was not studied using RNA-Seq expression data.

ChIP-Seq

Sorex araneus was not studied using ChIP-Seq data.

EST

Sorex araneus was not studied using EST data.

TSS

Sorex araneus was not studied using FANTOM5 data.

Lab

retro_sara_571 was not experimentally validated.

Homology

Retrocopy orthology:

Sorex araneus 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 10 parental genes, and 20 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	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,