RetrogeneDB ID: retro_mmus_264

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 18:46607699..46608134(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMUSG00000057561
• Aliases: Eif1a, C76390, Ef1a, Eftu, Eif4c, eIF-1A, eIF-4C
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: Eif1ax
• Ensembl ID: ENSMUSG00000067194
• Aliases: None
• Description: eukaryotic translation initiation factor 1A, X-linked [Source:MGI Symbol;Acc:MGI:1913485]

Sequence

>retro_mmus_264
ATGCCAAAGAATAAAGGCAAAGGAGGCAAAAACAGGCGCAGAGGTAAAAATGAAAATGAATCTGAGAAAAGAGAGTTGGT
GTTTAAAGAGGATGGGCAGGAGTATGCTCAGGTGATCAAAATGCTGGGAAATGGACGGTTGGAAGCAATGTGCTTTGACG
GTGTGAGGAGGCTGTGCCATATAAGAGGGAAGCTGAGAAAAAAGGTTTGGATAAATACCTCGGACATTATATTGATTGGT
CTACGAGACTATCAAGATAACAAAGCTGATGTAATCTTAAAGTATAATGCAGATGAAGCAAGAAGTCTGAAGGCCTATGG
AGAACTTCCAGAACATGCCAAAATCAATGAAACGGACACATTTGGTCCTGGGGATGATGATGAAATCCAATTTGATGATA
TTGGAGATGATGATGAAGACATTGATGACATCTAG

Alignment

ORF - retro_mmus_264 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 98.61 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MPKNKGKGGKNRRRGKNENESEKRELVFKEDGQEYAQVIKMLGNGRLEAMCFDGVKRLCHIRGKLRKKVW
          MPKNKGKGGKNRRRGKNENESEKRELVFKEDGQEYAQVIKMLGNGRLEAMCFDGV.RLCHIRGKLRKKVW
Retrocopy MPKNKGKGGKNRRRGKNENESEKRELVFKEDGQEYAQVIKMLGNGRLEAMCFDGVRRLCHIRGKLRKKVW

Parental  INTSDIILVGLRDYQDNKADVILKYNADEARSLKAYGELPEHAKINETDTFGPGDDDEIQFDDIGDDDED
          INTSDIIL.GLRDYQDNKADVILKYNADEARSLKAYGELPEHAKINETDTFGPGDDDEIQFDDIGDDDED
Retrocopy INTSDIILIGLRDYQDNKADVILKYNADEARSLKAYGELPEHAKINETDTFGPGDDDEIQFDDIGDDDED

Parental  IDDI
          IDDI
Retrocopy IDDI

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	10.89 RPM	131.51 RPM
SRP007412_cerebellum	13.76 RPM	111.85 RPM
SRP007412_heart	5.76 RPM	56.16 RPM
SRP007412_kidney	20.73 RPM	63.35 RPM
SRP007412_liver	27.42 RPM	31.87 RPM
SRP007412_testis	28.54 RPM	55.85 RPM

ChIP-Seq

RNA Polymerase II activity may be related with retro_mmus_264 in 1 libraries

ENCODE library ID	Target	ChIP-Seq Peak coordinates
ENCFF001YKA	POLR2A	18:46600603..46613685

EST

1 EST(s) were mapped to retro_mmus_264 retrocopy

EST ID	Start	End	Identity	Match	Mis-match	Score
DY248008	46607698	46607816	99.2	117	1	116

TSS

No TSS is located nearby retro_mmus_264 retrocopy 5' end.

Lab

retro_mmus_264 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_264 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Rattus norvegicus	retro_rnor_24

---

Parental genes homology:

Parental genes homology involve 28 parental genes, and 47 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000012660	1 retrocopy	retro_acar_151,
Ailuropoda melanoleuca	ENSAMEG00000016604	1 retrocopy	retro_amel_1421,
Bos taurus	ENSBTAG00000017633	3 retrocopies	retro_btau_1293, retro_btau_293, retro_btau_381,
Callithrix jacchus	ENSCJAG00000005371	1 retrocopy	retro_cjac_66,
Dipodomys ordii	ENSDORG00000011536	1 retrocopy	retro_dord_484,
Equus caballus	ENSECAG00000006469	2 retrocopies	retro_ecab_464, retro_ecab_634,
Erinaceus europaeus	ENSEEUG00000007518	3 retrocopies	retro_eeur_408, retro_eeur_567, retro_eeur_686,
Homo sapiens	ENSG00000173674	2 retrocopies	retro_hsap_1431, retro_hsap_350,
Gorilla gorilla	ENSGGOG00000012186	3 retrocopies	retro_ggor_1103, retro_ggor_363, retro_ggor_968,
Latimeria chalumnae	ENSLACG00000015565	1 retrocopy	retro_lcha_65,
Microcebus murinus	ENSMICG00000004110	2 retrocopies	retro_mmur_183, retro_mmur_197,
Myotis lucifugus	ENSMLUG00000012977	2 retrocopies	retro_mluc_250, retro_mluc_3,
Macaca mulatta	ENSMMUG00000000193	1 retrocopy	retro_mmul_1590,
Monodelphis domestica	ENSMODG00000027820	1 retrocopy	retro_mdom_274,
Mus musculus	ENSMUSG00000067194	1 retrocopy	retro_mmus_264 ,
Nomascus leucogenys	ENSNLEG00000009913	1 retrocopy	retro_nleu_1845,
Otolemur garnettii	ENSOGAG00000008182	1 retrocopy	retro_ogar_128,
Pongo abelii	ENSPPYG00000020176	1 retrocopy	retro_pabe_1185,
Pan troglodytes	ENSPTRG00000022504	1 retrocopy	retro_ptro_978,
Pteropus vampyrus	ENSPVAG00000003521	2 retrocopies	retro_pvam_780, retro_pvam_92,
Rattus norvegicus	ENSRNOG00000005736	1 retrocopy	retro_rnor_24,
Sorex araneus	ENSSARG00000013528	1 retrocopy	retro_sara_324,
Sarcophilus harrisii	ENSSHAG00000010995	1 retrocopy	retro_shar_707,
Sus scrofa	ENSSSCG00000029864	1 retrocopy	retro_sscr_948,
Ictidomys tridecemlineatus	ENSSTOG00000026117	1 retrocopy	retro_itri_1839,
Tupaia belangeri	ENSTBEG00000017492	6 retrocopies	retro_tbel_1604, retro_tbel_312, retro_tbel_3762, retro_tbel_4137, retro_tbel_4712, retro_tbel_798,
Tursiops truncatus	ENSTTRG00000002012	1 retrocopy	retro_ttru_1009,
Vicugna pacos	ENSVPAG00000009927	4 retrocopies	retro_vpac_47, retro_vpac_531, retro_vpac_550, retro_vpac_590,