RetrogeneDB ID: retro_mmus_2254

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 3:56828321..56828787(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: 1110059E24Rik
• Ensembl ID: ENSMUSG00000035171
• Aliases: None
• Description: RIKEN cDNA 1110059E24 gene [Source:MGI Symbol;Acc:MGI:1913456]

Sequence

>retro_mmus_2254
ATGAGTTCCCAGAAAGGAAACATGACTCGATCCTGGCCTCAGACTCACCAGAGTACGTTCACCTTCAAAAATGACAAGTT
TGATAAGAGTGTTCAGACCAAGAAAATTAATGCAAAACGTCATGATGGAGTATGTCAATGCTGCAAAGAAGTTCTTGAAT
GGCTTGTAAAATACAGCAAATACAAGCCACTGTCAAAGCCTAAGAAATGTGTTAATGTTTACAAAAGACAGTAAAGGACT
CTTACCACATAATGTGTAGACCACGTGCCTGTGAACTCGAAGTTTGTGCAAAATGTAGAAAGAAAGAAGAGATCATTATT
CCATTTAATAAAGAACCAGAAACTTAAGAAAAATTACTGAAAATGAAGGTTCTAACAATAGAAGAAGCTGCAGACAGAAG
GAAGACAGTGATAAGGACTTAGATGCTGAGTCTGACTCTGATGTCGAGGATGGGGAGACTCAGGCC

Alignment

ORF - retro_mmus_2254 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 79.75 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MSSQKGNVTRSRPQKHQNTFTFKNDKFDKSVQTKKINAKLHDGVCQRCKEVLEWRVKYSKYKPLSKPKKC
          MSSQKGN.TRS.PQ.HQ.TFTFKNDKFDKSVQTKKINAK.HDGVCQ.CKEVLEW.VKYSKYKPLSKPKKC
Retrocopy MSSQKGNMTRSWPQTHQSTFTFKNDKFDKSVQTKKINAKRHDGVCQCCKEVLEWLVKYSKYKPLSKPKKC

Parental  VK-CLQKTVKDSYHIMCRPCACELEVCAKCGKKEEIVIPFNKEPDAPE-NTENEGSGHRRRCGR-KEDSD
          V..CLQKTVKDSYHIMCRP.ACELEVCAKC.KKEEI.IPFNKEP...E...........RR..R.KEDSD
Retrocopy VN<CLQKTVKDSYHIMCRPRACELEVCAKCRKKEEIIIPFNKEPET*E<KITENEGSNNRRSCRQKEDSD

Parental  EDLDAESDSDGEDGDTQA
          .DLDAESDSD.EDG.TQA
Retrocopy KDLDAESDSDVEDGETQA

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	13.64 RPM
SRP007412_cerebellum	0.00 RPM	15.46 RPM
SRP007412_heart	0.00 RPM	5.45 RPM
SRP007412_kidney	0.00 RPM	10.07 RPM
SRP007412_liver	0.00 RPM	17.20 RPM
SRP007412_testis	0.00 RPM	9.15 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_2254 was not detected

EST

No EST(s) were mapped for retro_mmus_2254 retrocopy.

TSS

No TSS is located nearby retro_mmus_2254 retrocopy 5' end.

Lab

retro_mmus_2254 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_2254 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 19 parental genes, and 41 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000007254	1 retrocopy	retro_amel_730,
Bos taurus	ENSBTAG00000006831	1 retrocopy	retro_btau_39,
Canis familiaris	ENSCAFG00000001820	1 retrocopy	retro_cfam_2126,
Callithrix jacchus	ENSCJAG00000001441	2 retrocopies	retro_cjac_1283, retro_cjac_1374,
Cavia porcellus	ENSCPOG00000025848	2 retrocopies	retro_cpor_1538, retro_cpor_316,
Felis catus	ENSFCAG00000031942	1 retrocopy	retro_fcat_1955,
Homo sapiens	ENSG00000155621	2 retrocopies	retro_hsap_2104, retro_hsap_2895,
Myotis lucifugus	ENSMLUG00000024309	2 retrocopies	retro_mluc_2449, retro_mluc_2526,
Macaca mulatta	ENSMMUG00000018881	2 retrocopies	retro_mmul_670, retro_mmul_988,
Mustela putorius furo	ENSMPUG00000008971	1 retrocopy	retro_mputfur_1413,
Mus musculus	ENSMUSG00000035171	6 retrocopies	retro_mmus_1049, retro_mmus_2254 , retro_mmus_2286, retro_mmus_2781, retro_mmus_2941, retro_mmus_3698,
Nomascus leucogenys	ENSNLEG00000001023	1 retrocopy	retro_nleu_1272,
Oryctolagus cuniculus	ENSOCUG00000024578	2 retrocopies	retro_ocun_703, retro_ocun_766,
Otolemur garnettii	ENSOGAG00000011302	1 retrocopy	retro_ogar_979,
Pongo abelii	ENSPPYG00000029745	2 retrocopies	retro_pabe_1996, retro_pabe_2397,
Pan troglodytes	ENSPTRG00000021018	2 retrocopies	retro_ptro_1543, retro_ptro_1958,
Rattus norvegicus	ENSRNOG00000027161	5 retrocopies	retro_rnor_1898, retro_rnor_2010, retro_rnor_2242, retro_rnor_2859, retro_rnor_2960,
Sorex araneus	ENSSARG00000004523	1 retrocopy	retro_sara_260,
Tupaia belangeri	ENSTBEG00000015556	6 retrocopies	retro_tbel_1998, retro_tbel_200, retro_tbel_2406, retro_tbel_2410, retro_tbel_3539, retro_tbel_940,