RetrogeneDB ID: retro_mmus_1549

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 17:16847394..16848076(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Laptm4b
• Ensembl ID: ENSMUSG00000022257
• Aliases: Laptm4b, C330023P13Rik, LAPTM4beta
• Description: lysosomal-associated protein transmembrane 4B [Source:MGI Symbol;Acc:MGI:1890494]

Sequence

>retro_mmus_1549
ATGAACATGGTCGCTCCCTGGACTCGGTTCTACTCCCACAGCTGCTGTTTGTGCTGCCATGTCCACACCGGCACCATCCT
GCTAAGCGTCTGGTACCTGATCATCAATGCTGTGGTCCTGCTGATCCTGCTGAGTGCCCTGGCAGATCCCGATCAGTATC
ACTTTTCAGGCTCTGAACTAGGAGGGGAGTTTGAGTTCATGGATGATGCCAACATGTGCATTGCTATAGCAATCTCTCTC
CTCATGATCCTGATATGTGCCATGGCTAATTACGGTGCATACAAGCAACATGCTGCCTGGATCATCCCATTCTTCTGTTA
CCAGATCTTTGATTTTGCCCTGAATACTTTGGTTGCAATCACCGTGCTTATCTATCCAAACTCCATTCAGGAATACATAC
GACAGCTGGCTCCTAGCTTTCCCTACAGAGATGATATAATGTCCGTGAATCCTACCTATTTGGTCCTTATTATTCTTCTG
TTTATCGGCATTCTTTTGACACTTAAGGGCTACTTGATTAGCTGCATTTTGGAGCTGCTACAGGTACATCAATGGCAGGA
ACTCCTCCGATGTCCTGGTTTACGTTACCAGCAATGATACCACAGTGCTACTGCCTCCGTACGATGATGCTACTGCTGTG
CCTAGCACTGCCAAGTAGCCACCACCACCTTACTTGTCTGCC

Alignment

ORF - retro_mmus_1549 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 94.74 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MKMVAPWTRFYSHSCCLCCHVRTGTILLGVWYLIINAVVLLILLSALADPNQYHFSGSELGGEFEFMDDA
          M.MVAPWTRFYSHSCCLCCHV.TGTILL.VWYLIINAVVLLILLSALADP.QYHFSGSELGGEFEFMDDA
Retrocopy MNMVAPWTRFYSHSCCLCCHVHTGTILLSVWYLIINAVVLLILLSALADPDQYHFSGSELGGEFEFMDDA

Parental  NMCIAIAISLLMILICAMATYGAYKQHAAWIIPFFCYQIFDFALNTLVAITVLVYPNSIQEYIRQLPPSF
          NMCIAIAISLLMILICAMA.YGAYKQHAAWIIPFFCYQIFDFALNTLVAITVL.YPNSIQEYIRQL.PSF
Retrocopy NMCIAIAISLLMILICAMANYGAYKQHAAWIIPFFCYQIFDFALNTLVAITVLIYPNSIQEYIRQLAPSF

Parental  PYRDDIMSVNPTCLVLIILLFIGILLTLKGYLISCV-WSCYRYINGRNSSDVLVYVTSNDTTVLLPPYDD
          PYRDDIMSVNPT.LVLIILLFIGILLTLKGYLISC..WSCYRYINGRNSSDVLVYVTSNDTTVLLPPYDD
Retrocopy PYRDDIMSVNPTYLVLIILLFIGILLTLKGYLISCI>WSCYRYINGRNSSDVLVYVTSNDTTVLLPPYDD

Parental  ATAVPSTAKEPPPPYVSA
          ATAVPSTAK.PPPPY.SA
Retrocopy ATAVPSTAK*PPPPYLSA

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	0.26 RPM	70.74 RPM
SRP007412_cerebellum	0.22 RPM	68.26 RPM
SRP007412_heart	0.06 RPM	50.68 RPM
SRP007412_kidney	0.21 RPM	51.92 RPM
SRP007412_liver	0.08 RPM	13.49 RPM
SRP007412_testis	0.55 RPM	55.71 RPM

ChIP-Seq

RNA Polymerase II activity near the 5' end of retro_mmus_1549 was not detected

EST

No EST(s) were mapped for retro_mmus_1549 retrocopy.

TSS

No TSS is located nearby retro_mmus_1549 retrocopy 5' end.

Lab

retro_mmus_1549 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_1549 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 6 parental genes, and 12 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000016959	3 retrocopies	retro_btau_1493, retro_btau_1759, retro_btau_786,
Callithrix jacchus	ENSCJAG00000031235	3 retrocopies	retro_cjac_1368, retro_cjac_1664, retro_cjac_3027,
Myotis lucifugus	ENSMLUG00000003618	1 retrocopy	retro_mluc_1182,
Mus musculus	ENSMUSG00000022257	1 retrocopy	retro_mmus_1549 ,
Oryctolagus cuniculus	ENSOCUG00000013689	1 retrocopy	retro_ocun_627,
Otolemur garnettii	ENSOGAG00000000512	3 retrocopies	retro_ogar_1977, retro_ogar_2856, retro_ogar_2902,