RetrogeneDB ID: retro_sara_308

Retrocopy location

• Organism: Shrew (Sorex araneus)
• Coordinates: scaffold_157342:1723..2501(-)
• 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_308
TTTGGCTCAGTTAATGGAAAAATTGAGATAGAGATCAAGATCAACCATGGAGGAGAAGTAAACAGGGCACGTTACATGCC
TCAGAACTCTTGCATCATTGCAACAAAAACTCCATCCAGTGATGTTCTTGTTTTTGACTATACAAAGCATCCTTCGAAAC
CAGACCCTTCTGGTGAGTGCAACCCAGACTTGCATCTCCCGGGACATCAGAAGGAAGGATATGGGCTTTCTTGGAACCCA
AATCTCAGTGGGCACTTACTTAGTGCTTCCGATGACCATACCATCTGCCTGTGGGACATCAGTGCTGTTCCAAAGGAAGG
AAAAATTGTGGATGCCAAGACCATCTTTACAGGCCACACAGCAGTAGAGAGGATGTTTCCTGGCATCTGCTCCATGAGTC
TTTGTTGGTTCAGTTGCCAATGATCAGAAACTTATGATTTGGGATACTCATTCAAACAATACTTCCAAACCAAGCCACTC
AGTTGATGCTCACATTGCTGAAGTGAACTGCCTGTCTTTCAACCCTTACAGTGAGTTCATTCTTGCCACAGGATCGGCTG
ACAAGACTGTTGGCTTGTGGGATCTGAGAAATCTGAAACTTAAGTTGCATTCCTTTGAATCACACAAGGATAAAATATTC
CAGGTTCAGTGGTCACCTCACAATGAGACTATTTTGGCTTCCAGTGGAACTGATCGTAGACTGAATGTTTGGAACTTGAG
TAAAATTGGAGAAGAACAATCCCCAGAAGATGCAGAGGATGGGCCACCAGAATTACTG

Alignment

ORF - retro_sara_308 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 87.4 %
• Parental protein coverage: 55.36 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  FGSVTGKIECEIKINHEGEVNRARYMPQNPHIIATKTPSSDVLVFDYTKHPAKPDPSGECNPDLRLRGHQ
          FGSV.GKIE.EIKINH.GEVNRARYMPQN..IIATKTPSSDVLVFDYTKHP.KPDPSGECNPDL.L.GHQ
Retrocopy FGSVNGKIEIEIKINHGGEVNRARYMPQNSCIIATKTPSSDVLVFDYTKHPSKPDPSGECNPDLHLPGHQ

Parental  KEGYGLSWNSNLSGHLLSASDDHTRL--DINAGPKEGKIVDAKGIFTGHSAVV-EDVAWHLLHESLF-GS
          KEGYGLSWN.NLSGHLLSASDDHT....DI.A.PKEGKIVDAK.IFTGH.AV..EDV.WHLLHESL..GS
Retrocopy KEGYGLSWNPNLSGHLLSASDDHTICLWDISAVPKEGKIVDAKTIFTGHTAVE<EDVSWHLLHESLL<GS

Parental  VADDQKLMIWDTRSNTTSKPSHLVDAHTAEVNCLSFNPYSEFILATGSADKTVALWDLRNLKLKLHTFES
          VA.DQKLMIWDT.SN.TSKPSH.VDAH.AEVNCLSFNPYSEFILATGSADKTV.LWDLRNLKLKLH.FES
Retrocopy VANDQKLMIWDTHSNNTSKPSHSVDAHIAEVNCLSFNPYSEFILATGSADKTVGLWDLRNLKLKLHSFES

Parental  HKDEIFQVHWSPHNETILASSGTDRRLNVWDLSKIGEEQSAEDAEDGPPELL
          HKD.IFQV.WSPHNETILASSGTDRRLNVW.LSKIGEEQS.EDAEDGPPELL
Retrocopy HKDKIFQVQWSPHNETILASSGTDRRLNVWNLSKIGEEQSPEDAEDGPPELL

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_308 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,