RetrogeneDB ID: retro_mmus_390

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 1:175920651..175921692(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Becn1
• Ensembl ID: ENSMUSG00000035086
• Aliases: None
• Description: beclin 1, autophagy related [Source:MGI Symbol;Acc:MGI:1891828]

Sequence

>retro_mmus_390
GGTGAATCTGCCTCCATGAGAACTATGAACACTATCCAAAATACTGTCTTAGAGACCTTCGAAATCCTCTCCGACCAAAA
GGTGGTGGACCACCCGCTGTGTGTGGACTGTACCGACCATCTTCTGATGCAACTAGACGACCAGCTCGCTCTCCTGGCAT
CTGACAACCAGAAGTACAAAAGTTTCCAGGACAGAGAGTTGCTGGTGAGTGAGGAAGAGAGGGAGGCGCTACACGCGGAG
CTTTGTGCCGAACTGTCCAGTCTGGAGCAGGAGGAAGCAAGGCTGACCCAGGAGCTAGAGGATTTAGACGGCCATCATGC
AAGGGTAGCCGCTGAACTCAGAGCAGCCCAGGCCGAGAGCAAGGAGCTGTATAAACAGCATGAGCAGCACAGGGTCGAGT
ACTCTGTTTTCAAGATGGAACAGCTGGAGCTGATGGACCAGCTGAGCAGTGTGGAGAACCAGCTGACGTATGCCCTGAGT
CAGCAGTACCGCTTAAGACAGACCAATATCTTCAACGCCACATTTACCATTTCAGATGAGGGTCCCTTGGGCGTTATCAA
CAATTTTAGGCTGGGCTGTCTCCCCGGGGTCCGGGTGGGCTGGACTGAGATCAGTTCTGCCTGGGGACAGACAGTCTTAC
TGCTCTTCAGCTTGTCCAAGATAGCTGGACTGCAATTCCAGAGATATCAACTGGTTCCCTTTGGGGACCATTCCTATCTC
AAGTCCTTGACTGGTGATGGCGTGCTGCCCTTATTCTCTGATGGGAGCCACAGCGTCTTCTTGAATAACAAGTTTGACTG
TGGGATGAAGGCCTTCCTGGACTGTCTTCAGCAGTTTGTGGAGGAGATTGAGAGGGATGAGAGATGCCCCTGCCTGCCCT
ACAGGATCCATGTGAAGGAAGGGCTGATGGAGGATGTCTGGGACAGTGGGGAGTGCTGCTCCATCAGGACCCATCTGAAC
ACGGAGGAGGAGTGGTCCAGGGCTCTGAAATTCATGCTTTCGGACTTGAAGTTGATCCTTGCTTGGGCTTCCTTAAGGTA
C

Alignment

ORF - retro_mmus_390 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 50.14 %
• Parental protein coverage: 77.46 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  GEASDGGTMENLSRRLKVTGDLFDIMSGQTDVDHPLCEECTDTLLDQLDTQLNVTENECQNYK----RCL
          GE.....TM.........T...F.I.S.Q..VDHPLC..CTD.LL.QLD.QL.......Q.YK....R.L
Retrocopy GESASMRTMNTIQNTVLET---FEILSDQKVVDHPLCVDCTDHLLMQLDDQLALLASDNQKYKSFQDREL

Parental  EILEQMNEDDSEQLQRELKELALEEERLIQELEDVEKNRKVVAENLEKVQAEAERLDQEEAQYQREYSEF
          ...E...E.....L..EL..L..EE.RL.QELED.......VA..L...QAE...L.....Q...EYS.F
Retrocopy LVSEEEREALHAELCAELSSLEQEEARLTQELEDLDGHHARVAAELRAAQAESKELYKQHEQHRVEYSVF

Parental  KRQQLELDDELKSVENQVRYAQIQLDKLKKTNVFNATFHIWHSGQFGTINNFRLGRLPSVPVEWNEINAA
          K..QLEL.D.L.SVENQ..YA..Q...L..TN.FNATF.I...G..G.INNFRLG.LP.V.V.W.EI..A
Retrocopy KMEQLELMDQLSSVENQLTYALSQQYRLRQTNIFNATFTISDEGPLGVINNFRLGCLPGVRVGWTEISSA

Parental  WGQTVLLLHALANKMGLKFQRYRLVPYGNHSYLESLTDKSKELPLYCSGGLRFFWDNKFDHAMVAFLDCV
          WGQTVLLL..L....GL.FQRY.LVP.G.HSYL.SLT.....LPL...G....F..NKFD..M.AFLDC.
Retrocopy WGQTVLLLFSLSKIAGLQFQRYQLVPFGDHSYLKSLTGDG-VLPLFSDGSHSVFLNNKFDCGMKAFLDCL

Parental  QQFKEEVEKGETRFCLPYRMDVEKGKIEDTGGSGGSYSIKTQFNSEEQWTKALKFMLTNLKWGLAWVSSQ
          QQF.EE.E..E...CLPYR..V..G..ED...SG...SI.T..N.EE.W..ALKFML..LK..LAW.S..
Retrocopy QQFVEEIERDERCPCLPYRIHVKEGLMEDVWDSGECCSIRTHLNTEEEWSRALKFMLSDLKLILAWASLR

Parental  F
          .
Retrocopy Y

Legend:

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

Expression

RNA-Seq

Expression validation based on RNA-Seq data:

Library	Retrocopy expression	Parental gene expression
SRP007412_brain	0.00 RPM	62.94 RPM
SRP007412_cerebellum	0.04 RPM	61.01 RPM
SRP007412_heart	0.00 RPM	40.91 RPM
SRP007412_kidney	0.02 RPM	81.70 RPM
SRP007412_liver	0.00 RPM	45.47 RPM
SRP007412_testis	0.14 RPM	86.81 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_390 was not detected

EST

No EST(s) were mapped for retro_mmus_390 retrocopy.

TSS

No TSS is located nearby retro_mmus_390 retrocopy 5' end.

Lab

retro_mmus_390 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_390 has 0 orthologous retrocopies within eutheria group .

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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,