RetrogeneDB ID: retro_mmus_2505

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 4:115416081..115416466(-)
• Located in intron of: ENSMUSG00000078597

Retrocopy information

• Ensembl ID: ENSMUSG00000084415
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Mcts1
• Ensembl ID: ENSMUSG00000000355
• Aliases: Mcts1, 1500019M23Rik, MCT-1
• Description: malignant T cell amplified sequence 1 [Source:MGI Symbol;Acc:MGI:1916245]

Sequence

>retro_mmus_2505
ATTTTCAAAAACCATGAAAACACAGAAATCTTTACAGTAAATGGAGAATTACTGTCTTTTAGACAAAGAGAAGGGACTTT
TTAAAATCCAACCTTAGGATGACTTCATATTCTTTTATCATATCACAACAGTGGATTAATAAAAGAGTCATTAACTTGTA
CTTAGTGGATCAAATATCATGTTTCCAGGGTTAACATCTGGGTCTAAGCTTTACCCTGCTGCAGAAGATACTATTGTTGC
AAACGTGTCAGAAGGAAAGAAACATGCTGTATGTATTGGAGTCCTGAAGATATATGCAGAACATTTTGAGAAAATCAACA
AAGGAATTAGCATTGAAAATATCCATTATTTAAATGATATGCGATGGCATAGGGAGATATATAAA

Alignment

ORF - retro_mmus_2505 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 59.85 %
• Parental protein coverage: 71.82 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  IVRCHEHIEILTVNGELLFFRQREGP-FYPTLRLLHKYPFILPHQQVDKGAIKF-VLSGANIMCPGLTSP
          I...HE..EI.TVNGELL.FRQREG..F.........Y.FI...Q...K..I...VLSG.NIM.PGLTS.
Retrocopy IFKNHENTEIFTVNGELLSFRQREGT<FLKSNLRMTSYSFIISQQWINKRVINL<VLSGSNIMFPGLTS-

Parental  GAKLYPAAVDTIVAIMAEGKQHALCVGVMKMSAEDIEKVNKGIGIENIHYLNDGLWHMKTYK
          G.KLYPAA.DTIVA...EGK.HA.C.GV.K..AE..EK.NKGI.IENIHYLND..WH...YK
Retrocopy GSKLYPAAEDTIVANVSEGKKHAVCIGVLKIYAEHFEKINKGISIENIHYLNDMRWHREIYK

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	27.01 RPM
SRP007412_cerebellum	0.00 RPM	14.46 RPM
SRP007412_heart	0.00 RPM	8.44 RPM
SRP007412_kidney	0.00 RPM	14.51 RPM
SRP007412_liver	0.00 RPM	14.53 RPM
SRP007412_testis	0.00 RPM	1.69 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_2505 was not detected

EST

No EST(s) were mapped for retro_mmus_2505 retrocopy.

TSS

No TSS is located nearby retro_mmus_2505 retrocopy 5' end.

Lab

retro_mmus_2505 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_2505 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 26 parental genes, and 35 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000034992	1 retrocopy	retro_btau_116,
Canis familiaris	ENSCAFG00000018545	1 retrocopy	retro_cfam_94,
Cavia porcellus	ENSCPOG00000005502	1 retrocopy	retro_cpor_1411,
Equus caballus	ENSECAG00000014597	1 retrocopy	retro_ecab_697,
Erinaceus europaeus	ENSEEUG00000007258	1 retrocopy	retro_eeur_197,
Echinops telfairi	ENSETEG00000015462	1 retrocopy	retro_etel_19,
Felis catus	ENSFCAG00000008448	2 retrocopies	retro_fcat_1009, retro_fcat_310,
Homo sapiens	ENSG00000232119	1 retrocopy	retro_hsap_2422,
Gorilla gorilla	ENSGGOG00000009420	1 retrocopy	retro_ggor_1507,
Macropus eugenii	ENSMEUG00000014328	1 retrocopy	retro_meug_1518,
Myotis lucifugus	ENSMLUG00000015101	1 retrocopy	retro_mluc_16,
Macaca mulatta	ENSMMUG00000009043	1 retrocopy	retro_mmul_626,
Monodelphis domestica	ENSMODG00000010354	1 retrocopy	retro_mdom_203,
Mustela putorius furo	ENSMPUG00000001407	1 retrocopy	retro_mputfur_98,
Mus musculus	ENSMUSG00000000355	3 retrocopies	retro_mmus_2504, retro_mmus_2505 , retro_mmus_69,
Nomascus leucogenys	ENSNLEG00000015021	1 retrocopy	retro_nleu_2442,
Oryctolagus cuniculus	ENSOCUG00000014315	1 retrocopy	retro_ocun_212,
Pongo abelii	ENSPPYG00000020687	2 retrocopies	retro_pabe_1786, retro_pabe_1833,
Pan troglodytes	ENSPTRG00000022241	1 retrocopy	retro_ptro_1396,
Pteropus vampyrus	ENSPVAG00000013249	3 retrocopies	retro_pvam_1323, retro_pvam_645, retro_pvam_867,
Rattus norvegicus	ENSRNOG00000002563	2 retrocopies	retro_rnor_1841, retro_rnor_957,
Ictidomys tridecemlineatus	ENSSTOG00000011496	2 retrocopies	retro_itri_1136, retro_itri_1468,
Tupaia belangeri	ENSTBEG00000010666	2 retrocopies	retro_tbel_1485, retro_tbel_4265,
Tarsius syrichta	ENSTSYG00000001440	1 retrocopy	retro_tsyr_55,
Tursiops truncatus	ENSTTRG00000007208	1 retrocopy	retro_ttru_1587,
Vicugna pacos	ENSVPAG00000001801	1 retrocopy	retro_vpac_138,