RetrogeneDB ID: retro_sara_136

Retrocopy location

• Organism: Shrew (Sorex araneus)
• Coordinates: GeneScaffold_4067:34174..35179(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: BECN1
• Ensembl ID: ENSSARG00000000367
• Aliases: None
• Description: beclin 1, autophagy related [Source:HGNC Symbol;Acc:1034]

Sequence

>retro_sara_136
GAGGTGAGGGTCAGTGGAGACCTTTTTGACATCATGTTGGGCCAGACAGATGAGGATCACCCCCTGTGTGAGGAATGCAC
AGACACTCTCTTAGACCAGCTGGACACTCAGCTCAACGTCACCGAAAATGAGTATCAGAACTACAAGCGCTGTTTGGAGA
TCTTGGAGCAAATGAATGAGGATGACAGTGAAGAGTTCTAGATGGAGCTGAAAGAGCTGGCCTTAGAGGAGGAGAGGCTG
ATCCAAGAGCTGGAAGTTGTGGAAAAGAACCGCAAGATAGTGGAGAAATCTGGAGAAGGTCCAGGCTGAAACCGAGTGAC
TGGATCAGGAGGAAGCCCAGTATCAGAGGGAGTACAGTGAATTTAACCGATAGCAGTTGGAGCTGGATGATGAACTGAAG
AGCGTAGAAAACAGATGCATTATGCCCAGATGCAACTGGACAAGCTGAAGAAAACCAACGTCTTTAATGCGACTTTCCAC
ATCTGGCACAGTGGACAGTTTGGCACGATCAATAACTTCAGGTTGGGTCACCTGCCCAGTGTTCCTGTGGAATGGAATGA
GATCAATGCTGCTTGGAGCAAGACCGTGTTGCTGCTCCATGCCCTGGCCAATAAGATGGGTCTGAAATTTCAGAGGTATC
GACTTTGTCCCTATGGAAACCATTCATATCTGGAGTTTCTGACAGACAAATCTAAGGAGCTGCCATTATACTGCTCAGGG
GGGTTGCGATTTTTCTGGGACAACAAGTTTGACCATGCGATGGTGGCTTTCCTGGACTGTGTGCAGAAGTTCAAAGAAGA
GGTGGAGAAAGGCAAGACACGTTTTTGTCTTCCTTACAGGATGGATGTGGAGAAAGGAAAGATTGAAGACACAGGAGGCA
GTGGCGGCTCCTATTCCATCAAAACCCAGTTTAACTCTGAGGAACAGTGGACAAAAGCTCTCAAATTTATGCTGACAAAT
CTTAAGTGGAGTCTTGCTTGGGTATCCTCACAATTTTTTAATAAG

Alignment

ORF - retro_sara_136 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 91.42 %
• Parental protein coverage: 74.67 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  KARVTGDLFDIMSGQTDVDHPLCEECTDTLLDQLDTQLNVTENECQNYKRCLEILEQMNEDDSEKLQMEL
          ..RV.GDLFDIM.GQTD.DHPLCEECTDTLLDQLDTQLNVTENE.QNYKRCLEILEQMNEDDSE...MEL
Retrocopy EVRVSGDLFDIMLGQTDEDHPLCEECTDTLLDQLDTQLNVTENEYQNYKRCLEILEQMNEDDSEEF*MEL

Parental  KELALEEERLIQELEDVEKNRKIVAE-NLEKVQAEAERLDQEEAQYQREYSEFKRQQLELDDELKSVEN-
          KELALEEERLIQELE.VEKNRK...E.NLEKVQAE.E.LDQEEAQYQREYSEF.R.QLELDDELKSVEN.
Retrocopy KELALEEERLIQELEVVEKNRK-IVE>NLEKVQAETE*LDQEEAQYQREYSEFNR*QLELDDELKSVEN<

Parental  QMRYAQMQLDKLKKTNVFNATFHIWHSGQFGTINNFRLGRLPSVPVEWNEINAAWGQTVLLLHALANKMG
          QM.YAQMQLDKLKKTNVFNATFHIWHSGQFGTINNFRLG.LPSVPVEWNEINAAW..TVLLLHALANKMG
Retrocopy QMHYAQMQLDKLKKTNVFNATFHIWHSGQFGTINNFRLGHLPSVPVEWNEINAAWSKTVLLLHALANKMG

Parental  LKFQRYRLVPYGNHSYLESLTDKSKELPLYCSGGLRFFWDNKFDHAMVAFLDCVQQFKEEVEKGETRFCL
          LKFQRYRL.PYGNHSYLE.LTDKSKELPLYCSGGLRFFWDNKFDHAMVAFLDCVQ.FKEEVEKG.TRFCL
Retrocopy LKFQRYRLCPYGNHSYLEFLTDKSKELPLYCSGGLRFFWDNKFDHAMVAFLDCVQKFKEEVEKGKTRFCL

Parental  PYRMDVEKGKIEDTGGSGGSYSIKTQFNSEEQWTKALKFMLTNLKWGLAWVSSQFYNK
          PYRMDVEKGKIEDTGGSGGSYSIKTQFNSEEQWTKALKFMLTNLKW.LAWVSSQF.NK
Retrocopy PYRMDVEKGKIEDTGGSGGSYSIKTQFNSEEQWTKALKFMLTNLKWSLAWVSSQFFNK

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_136 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 17 parental genes, and 19 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000006867	1 retrocopy	retro_amel_16,
Bos taurus	ENSBTAG00000019914	1 retrocopy	retro_btau_226,
Dipodomys ordii	ENSDORG00000000956	1 retrocopy	retro_dord_675,
Felis catus	ENSFCAG00000013136	1 retrocopy	retro_fcat_62,
Homo sapiens	ENSG00000126581	1 retrocopy	retro_hsap_335,
Macropus eugenii	ENSMEUG00000011700	1 retrocopy	retro_meug_600,
Macaca mulatta	ENSMMUG00000029971	1 retrocopy	retro_mmul_81,
Monodelphis domestica	ENSMODG00000015064	1 retrocopy	retro_mdom_1778,
Mus musculus	ENSMUSG00000035086	1 retrocopy	retro_mmus_390,
Nomascus leucogenys	ENSNLEG00000011840	1 retrocopy	retro_nleu_1776,
Oryctolagus cuniculus	ENSOCUG00000015964	3 retrocopies	retro_ocun_1021, retro_ocun_1732, retro_ocun_218,
Procavia capensis	ENSPCAG00000014049	1 retrocopy	retro_pcap_345,
Pan troglodytes	ENSPTRG00000022819	1 retrocopy	retro_ptro_268,
Sorex araneus	ENSSARG00000000367	1 retrocopy	retro_sara_136 ,
Sus scrofa	ENSSSCG00000017386	1 retrocopy	retro_sscr_75,
Ictidomys tridecemlineatus	ENSSTOG00000012612	1 retrocopy	retro_itri_25,
Tursiops truncatus	ENSTTRG00000011716	1 retrocopy	retro_ttru_595,