RetrogeneDB ID: retro_mmus_1018

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 13:62035419..62036163(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMUSG00000074868
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: 4933434E20Rik
• Ensembl ID: ENSMUSG00000027942
• Aliases: 4933434E20Rik, 5730552F22Rik, AI462154, NICE-3, NS5ATP4
• Description: RIKEN cDNA 4933434E20 gene [Source:MGI Symbol;Acc:MGI:1914027]

Sequence

>retro_mmus_1018
ATGGCATCTAGTAGTAACTGGCTTTCTGGAGTGAATGTCGTGCTGGTGATAGCGTACGGGAGCCTGGTATTCGTACTGCT
GTTTATTTTTGTGAAGAGACAAATCATGCGCTTTGCAATGAAATCTAGAAGGGGACCTCATGTTCCTGTAGGACACAATG
CCCCCAAGGACTTAAAAGAGATCGATATTCGACTATCCAGGGTTCAAGATATCAAGTATGAACCCCAGCTCCTTGCAGAT
GATGATACCAGACTACTGCAGCTGGAAACCCAGGGGAATCAAAGTTGCTACAACTATCTATACAGAATGAAAGCTCTAGA
TGCTATCTGTGCCTCTGAGATCCCGTTCCATGCTGAAGGCTGGCACCCCTGTTCTTTCATGGGTAAGAATTTCCACTCCG
ACTTGCTAGATCTGAGAAACACTAGCACTCTTTTCAAGGGTGTTGGCAAGGCCCTCATTGATACTCTCCTGGATGGATAT
GAGACAGCTCGCTATGGGACAGGGGTCTTTGGCCAGAGTGAGTACTTGCGTTATCAAGAGGCCTTGAGTGAGCTGGCCAC
TGTGGTCAAAGCACGAATTGGAAGTTCTCAGAGACAACACCAGTCAGCAGCCAAAGACCTAACTCAGTCGCCAACAACAA
TCCAGGTCACATACCTGCCCTCCAGTCAGAAGAGCAAACGCCCTAATCACTTCCTAGAACTGAAGAGCTTTACAGACAAC
TATAACACACTGGAGAGCACTCTG

Alignment

ORF - retro_mmus_1018 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 94.47 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MASSSNWLSGVNVVLVMAYGSLVFVLLFIFVKRQIMRFAMKSRRGPHVPVGHNAPKDLKEEIDIRLSRVQ
          MASSSNWLSGVNVVLV.AYGSLVFVLLFIFVKRQIMRFAMKSRRGPHVPVGHNAPKDLKE.IDIRLSRVQ
Retrocopy MASSSNWLSGVNVVLVIAYGSLVFVLLFIFVKRQIMRFAMKSRRGPHVPVGHNAPKDLKE-IDIRLSRVQ

Parental  DIKYEPQLLADDDTRLLQLETQGNQSCYNYLYRMKALDAIRASEIPFHAEGRHPCSLMGKNFRSYLLDLR
          DIKYEPQLLADDDTRLLQLETQGNQSCYNYLYRMKALDAI.ASEIPFHAEG.HPCS.MGKNF.S.LLDLR
Retrocopy DIKYEPQLLADDDTRLLQLETQGNQSCYNYLYRMKALDAICASEIPFHAEGWHPCSFMGKNFHSDLLDLR

Parental  NTSTPFKGVGKALIDTLLDGYETARYGTGVFGQSEYLRYQEALSELATVVKARIGSSQRQHQSAAKDLTQ
          NTST.FKGVGKALIDTLLDGYETARYGTGVFGQSEYLRYQEALSELATVVKARIGSSQRQHQSAAKDLTQ
Retrocopy NTSTLFKGVGKALIDTLLDGYETARYGTGVFGQSEYLRYQEALSELATVVKARIGSSQRQHQSAAKDLTQ

Parental  SPEMSPTTIQVTYLPSSQKSKRPKHFLELKSFKDNYNTLESTL
          SP....TTIQVTYLPSSQKSKRP.HFLELKSF.DNYNTLESTL
Retrocopy SP----TTIQVTYLPSSQKSKRPNHFLELKSFTDNYNTLESTL

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	39.69 RPM
SRP007412_cerebellum	0.00 RPM	34.26 RPM
SRP007412_heart	0.00 RPM	37.23 RPM
SRP007412_kidney	0.00 RPM	41.29 RPM
SRP007412_liver	0.00 RPM	21.66 RPM
SRP007412_testis	0.00 RPM	64.90 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_1018 was not detected

EST

No EST(s) were mapped for retro_mmus_1018 retrocopy.

TSS

No TSS is located nearby retro_mmus_1018 retrocopy 5' end.

Lab

retro_mmus_1018 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_1018 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 14 parental genes, and 43 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000009722	1 retrocopy	retro_cjac_175,
Dipodomys ordii	ENSDORG00000005454	1 retrocopy	retro_dord_190,
Echinops telfairi	ENSETEG00000001056	15 retrocopies	retro_etel_1138, retro_etel_1318, retro_etel_1388, retro_etel_1633, retro_etel_2182, retro_etel_2205, retro_etel_2206, retro_etel_394, retro_etel_651, retro_etel_719, retro_etel_720, retro_etel_773, retro_etel_842, retro_etel_957, retro_etel_981,
Macropus eugenii	ENSMEUG00000002600	6 retrocopies	retro_meug_1149, retro_meug_1298, retro_meug_1439, retro_meug_1637, retro_meug_213, retro_meug_69,
Myotis lucifugus	ENSMLUG00000013338	1 retrocopy	retro_mluc_537,
Monodelphis domestica	ENSMODG00000017237	3 retrocopies	retro_mdom_1283, retro_mdom_2003, retro_mdom_323,
Mus musculus	ENSMUSG00000027942	6 retrocopies	retro_mmus_1014, retro_mmus_1018 , retro_mmus_1020, retro_mmus_1107, retro_mmus_1792, retro_mmus_490,
Otolemur garnettii	ENSOGAG00000012008	2 retrocopies	retro_ogar_2563, retro_ogar_38,
Ochotona princeps	ENSOPRG00000007244	2 retrocopies	retro_opri_426, retro_opri_586,
Pongo abelii	ENSPPYG00000000785	2 retrocopies	retro_pabe_3590, retro_pabe_969,
Rattus norvegicus	ENSRNOG00000017758	1 retrocopy	retro_rnor_139,
Sarcophilus harrisii	ENSSHAG00000012915	1 retrocopy	retro_shar_740,
Tupaia belangeri	ENSTBEG00000013866	1 retrocopy	retro_tbel_177,
Tarsius syrichta	ENSTSYG00000012777	1 retrocopy	retro_tsyr_91,