RetrogeneDB ID: retro_sara_360

Retrocopy location

• Organism: Shrew (Sorex araneus)
• Coordinates: scaffold_179601:71259..72048(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSSARG00000010093
• Aliases: None
• Description: None

Sequence

>retro_sara_360
GCCAGCACTTTCTCTGTGAATTTGAAAGATGGATTGTCTGACCTGATACCTAAGGTACAGGCCAGAATTAAAAACTTCAG
AGAGCAACATGGCAAGACAGCGGTGGGCTATATCACTGTTGGTATGATGTATGGTGGCATGAGAGGCATGAAGGGATTGG
TCTACAAAACATCAGTTCTTGGTCCTGATGAGGGTATCCGCTTCAGAGGCTACAGTATCTCAAAATGCCAAAAGCTGTTG
CCCAAGGCTAAGGGTGGGGGAAGAGACCTTGCCTAAGGTCTTATTTTGGCTGGTTGTAACAGGAAAAATCCCAACAGAAG
AACAGGTATCTTGGCTATCAAACTTGTGAGCAAAAAGGGCAGCTCTGCCTTCCCATGTTGTGACCATGCTGGACAACTCT
CCCAACAATCTACATCCAATGTCTCAACTCAGTGCAGCCATTACAGCCCTCAACAGTGAAAGTAATTTTGCTCAGGCATA
TCCAGAGGGTGTCCACCGAACCAAGTCCTGGGAGTTGGTTTACAAAGACTGTATGGATCTGATCGCAAAGCTACCTTGCG
TTGCAGCAAAGATATACCAAAATCTCTACTGGGAGGGCAGCAGCACTGGGGGCCATTGACTCTAAGCTGGACTGGTCCTA
CAATTTCACCAACACGTTAGGCTATCCTGATGCTAAGTTCACTGAGCTCATGCGCTTGTACCTCAGCATCCACAGTGACC
ATGAGTGTGGCAATGTAAGTGGCCCATACCAGCCACCTTTTGGGCAGTGCCCTTTTAGACCATTATGTG

Alignment

ORF - retro_sara_360 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.28 %
• Parental protein coverage: 95.97 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  ASASSVNLKDVLSDLIPKEQARIKNFRQQHGKTVVGQITVDMMYGGMRGMKGLVYETSVLDPDEGIRFRG
          AS..SVNLKD.LSDLIPK.QARIKNFR.QHGKT.VG.ITV.MMYGGMRGMKGLVY.TSVL.PDEGIRFRG
Retrocopy ASTFSVNLKDGLSDLIPKVQARIKNFREQHGKTAVGYITVGMMYGGMRGMKGLVYKTSVLGPDEGIRFRG

Parental  YSIPECQKLLPKAKGG-EEPLPEGLFWLLVTGKIPTEEQVSWLSKEWAKRAALPSHVVTMLDNFPNNLHP
          YSI..CQKLLPKAKGG.EE.LP..LFWL.VTGKIPTEEQVSWLS...AKRAALPSHVVTMLDN.PNNLHP
Retrocopy YSISKCQKLLPKAKGG>EETLPKVLFWLVVTGKIPTEEQVSWLSNL*AKRAALPSHVVTMLDNSPNNLHP

Parental  MSQLSAAITALNSESNFARAYAEGVHRTKYWELVYEDCMDLIAKLPCVAAKIYRNLYREGSS-IGAIDSK
          MSQLSAAITALNSESNFA.AY.EGVHRTK.WELVY.DCMDLIAKLPCVAAKIY.NLY.EGSS..GAIDSK
Retrocopy MSQLSAAITALNSESNFAQAYPEGVHRTKSWELVYKDCMDLIAKLPCVAAKIYQNLYWEGSS>LGAIDSK

Parental  LDWSHNFTNMLGYTDAKFTELMRLYLTIHSDHEGGNVS-AHTSHLVGSALSDPYL
          LDWS.NFTN.LGY.DAKFTELMRLYL.IHSDHE.GNVS.AHTSHL.GSAL.D.Y.
Retrocopy LDWSYNFTNTLGYPDAKFTELMRLYLSIHSDHECGNVS>AHTSHLLGSALLDHYV

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_360 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 21 parental genes, and 29 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000004371	1 retrocopy	retro_btau_386,
Canis familiaris	ENSCAFG00000000115	1 retrocopy	retro_cfam_765,
Choloepus hoffmanni	ENSCHOG00000000397	1 retrocopy	retro_chof_1803,
Callithrix jacchus	ENSCJAG00000011275	1 retrocopy	retro_cjac_2031,
Dasypus novemcinctus	ENSDNOG00000010907	2 retrocopies	retro_dnov_205, retro_dnov_468,
Echinops telfairi	ENSETEG00000012035	1 retrocopy	retro_etel_584,
Homo sapiens	ENSG00000062485	2 retrocopies	retro_hsap_1972, retro_hsap_3621,
Gorilla gorilla	ENSGGOG00000009096	2 retrocopies	retro_ggor_1432, retro_ggor_2445,
Macropus eugenii	ENSMEUG00000005657	2 retrocopies	retro_meug_1078, retro_meug_1304,
Microcebus murinus	ENSMICG00000017659	2 retrocopies	retro_mmur_1322, retro_mmur_394,
Macaca mulatta	ENSMMUG00000002483	2 retrocopies	retro_mmul_1502, retro_mmul_1840,
Mus musculus	ENSMUSG00000005683	1 retrocopy	retro_mmus_258,
Nomascus leucogenys	ENSNLEG00000017514	2 retrocopies	retro_nleu_1201, retro_nleu_809,
Oryctolagus cuniculus	ENSOCUG00000007216	1 retrocopy	retro_ocun_1183,
Pongo abelii	ENSPPYG00000004654	1 retrocopy	retro_pabe_2972,
Rattus norvegicus	ENSRNOG00000023520	1 retrocopy	retro_rnor_2518,
Sorex araneus	ENSSARG00000010093	2 retrocopies	retro_sara_360 , retro_sara_628,
Sus scrofa	ENSSSCG00000021091	1 retrocopy	retro_sscr_321,
Sus scrofa	ENSSSCG00000022858	1 retrocopy	retro_sscr_322,
Tupaia belangeri	ENSTBEG00000006425	1 retrocopy	retro_tbel_4652,
Tarsius syrichta	ENSTSYG00000004483	1 retrocopy	retro_tsyr_1659,