RetrogeneDB ID: retro_mmus_221

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 3:139128333..139128771(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMUSG00000090801
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: Nme2
• Ensembl ID: ENSMUSG00000020857
• Aliases: Nme2, NM23-H2, NM23B, nm23-M2
• Description: NME/NM23 nucleoside diphosphate kinase 2 [Source:MGI Symbol;Acc:MGI:97356]

Sequence

>retro_mmus_221
TTGGCCAGCCTCAAGCATACCTTCATTGCCATCAAGTTCGATGGCGTGCAGCATGGCCTGGTGGGAGGGATCATCAAGCG
CTTCAAGGAGAAGAGGTTCTGCCTGATGGCCGTGAAGTTCCTTTGGGCTTCTGAGGAACATCTGAAGCAGCGCTATGTTG
ACTGGAAAGACCATCCTTTCTTCCCGGGGCCGTTGAAGCACTTGAACTCAGGACACATAGGTGCCATGGTCTGGGAGGGG
CTCAATTTGGTGAAAAGAGGCCGAGTGATGTTGCGAGAGACCAATCCAGCATATTCTAAACCAGGCACTATTCGTGGGGA
ATCTTGCATTCAAGGTGGCAGGAACATCACTTGTGGCAGCGATTCAGTGGAGAGTCTATGGTTTAAGTCAGAAGAACTGG
TTGATTATAAGTCGCGTGCCCATGACTGGGGTTATGAG

Alignment

ORF - retro_mmus_221 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 72.8 %
• Parental protein coverage: 82.24 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MANLERTFIAIKPDGVQRGLVGEIIKRFEQKGFRLVAMKFLRASEEHLKQHYIDLKDRPFFPGLVKYMNS
          .A.L..TFIAIK.DGVQ.GLVG.IIKRF..K.F.L.A.KFL.ASEEHLKQ.Y.D.KD.PFFPG..K..NS
Retrocopy LASLKHTFIAIKFDGVQHGLVGGIIKRFKEKRFCLMAVKFLWASEEHLKQRYVDWKDHPFFPGPLKHLNS

Parental  GPVVAMVWEGLNVVKTGRVMLGETNPADSKPGTIRGDFCIQVGRNIIHGSDSVES
          G...AMVWEGLN.VK.GRVML.ETNPA.SKPGTIRG..CIQ.GRNI..GSDSVES
Retrocopy GHIGAMVWEGLNLVKRGRVMLRETNPAYSKPGTIRGESCIQGGRNITCGSDSVES

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	0.77 RPM
SRP007412_cerebellum	0.00 RPM	0.96 RPM
SRP007412_heart	0.00 RPM	4.26 RPM
SRP007412_kidney	0.00 RPM	1.79 RPM
SRP007412_liver	0.00 RPM	0.93 RPM
SRP007412_testis	0.00 RPM	0.64 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_221 was not detected

EST

No EST(s) were mapped for retro_mmus_221 retrocopy.

TSS

No TSS is located nearby retro_mmus_221 retrocopy 5' end.

Lab

retro_mmus_221 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_221 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Rattus norvegicus	retro_rnor_1708

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Parental genes homology:

Parental genes homology involve 21 parental genes, and 57 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000008022	3 retrocopies	retro_amel_1573, retro_amel_390, retro_amel_538,
Bos taurus	ENSBTAG00000047186	1 retrocopy	retro_btau_1329,
Equus caballus	ENSECAG00000021658	1 retrocopy	retro_ecab_404,
Erinaceus europaeus	ENSEEUG00000003783	2 retrocopies	retro_eeur_156, retro_eeur_5,
Felis catus	ENSFCAG00000006742	5 retrocopies	retro_fcat_1083, retro_fcat_1117, retro_fcat_1475, retro_fcat_216, retro_fcat_663,
Homo sapiens	ENSG00000011052	1 retrocopy	retro_hsap_1063,
Loxodonta africana	ENSLAFG00000007784	1 retrocopy	retro_lafr_636,
Myotis lucifugus	ENSMLUG00000016929	3 retrocopies	retro_mluc_1422, retro_mluc_1882, retro_mluc_637,
Monodelphis domestica	ENSMODG00000012580	1 retrocopy	retro_mdom_1811,
Mustela putorius furo	ENSMPUG00000015573	4 retrocopies	retro_mputfur_1236, retro_mputfur_1590, retro_mputfur_327, retro_mputfur_912,
Mus musculus	ENSMUSG00000020857	1 retrocopy	retro_mmus_221 ,
Mus musculus	ENSMUSG00000024177	1 retrocopy	retro_mmus_309,
Mus musculus	ENSMUSG00000032478	1 retrocopy	retro_mmus_2376,
Mus musculus	ENSMUSG00000091228	3 retrocopies	retro_mmus_2712, retro_mmus_3081, retro_mmus_581,
Oryctolagus cuniculus	ENSOCUG00000024946	1 retrocopy	retro_ocun_418,
Otolemur garnettii	ENSOGAG00000025331	9 retrocopies	retro_ogar_1326, retro_ogar_1875, retro_ogar_1997, retro_ogar_2373, retro_ogar_2393, retro_ogar_2779, retro_ogar_3299, retro_ogar_483, retro_ogar_95,
Rattus norvegicus	ENSRNOG00000002671	8 retrocopies	retro_rnor_1129, retro_rnor_1610, retro_rnor_1708, retro_rnor_1784, retro_rnor_1966, retro_rnor_2646, retro_rnor_2951, retro_rnor_628,
Sarcophilus harrisii	ENSSHAG00000014470	3 retrocopies	retro_shar_130, retro_shar_554, retro_shar_781,
Sus scrofa	ENSSSCG00000017591	1 retrocopy	retro_sscr_854,
Tupaia belangeri	ENSTBEG00000013053	6 retrocopies	retro_tbel_1271, retro_tbel_1386, retro_tbel_2497, retro_tbel_294, retro_tbel_4620, retro_tbel_820,
Tursiops truncatus	ENSTTRG00000007433	1 retrocopy	retro_ttru_1821,