RetrogeneDB ID: retro_mmus_1408

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 15:75967229..75968335(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Eif2s3x
• Ensembl ID: ENSMUSG00000035150
• Aliases: Eif2s3x, AA409828, AA547477, AI314668, Eif-2gx
• Description: eukaryotic translation initiation factor 2, subunit 3, structural gene X-linked [Source:MGI Symbol;Acc:MGI:1349431]

Sequence

>retro_mmus_1408
AGATCATGTGGAAGCAGTACACCAGATAAGTTTCCTACATACATTCTGGGGGCCAAAGGGAACTTCAAATTAGTCAGACA
TGTTTCCTTTGTTGACTGTCCTGGCCATGATATTTTGATGGCTACGATGCTGAACAGTGCAGTAGAGATGGATGCAGCTC
TTCTGTTGATAGCTAGTAATGAATCATGCCCTTGGCCCGAACACCTGACTGCTGTAGAAATCACGAAACTCAAGCATATT
TTGATCTTACAGAATAAAATTGATCTGGTAAAAGAAAGTCAGGCTAAGGAACAATATGAGCAAAATCTCGCATTTGTGCA
AGGAACGATAGCAGAAAGGGGCACCAATTATTCCAATTTCTGCTCAACTGAAGTATAATATTGAAGTTGTCTGTGAGTAT
ATAGTGAAGAAAATACCAGTGGCCCCAAGAGACTTTACTTCAGAGCCCCATCTCATTGTTATCAGTCCATCTGATGTCAA
CAAACCTGGCTGTGAAGTCGATGACCTTAAGGGAGGTATAGCTGGTGGTAGTATTCTAAAAGGAGTGTTAAAGGTATGCC
AGGAGATAGAAGTCAGACCCCGTATTGTCTCCAAAGATAGGGAAGGAAAACTCATGTGTAAACCAACCTTTTCCAATATT
GTGTCACTTTTTTGGGGGAAACATAATGATCTTCAGTATGCTGCCCCAGGTGGTCTCACTGGAGTTGGAACAAAGATCGG
CCCCACTGTGTGCTGAGCTGGTAGAATGGTGGGACAAGTGCTTGGTGCAGTTGGAGCGTTACCTGAAATATTCACAGAAC
TGGAAATCTCCTATTTCCTGCTTAAACGTCTTCTGGGTGTACGTACTGAAGGAGACAAGAAAGCAGCCAAGGTCCAAAAG
CTGTCTAAGAATGAAGTGCTTATGGTCAACATAGGATCCCTGTTGACAGGAGGAAGAGTTAGTGCTGTTAAGGCTGATTT
GGGCAAAATTGTTTTGACCAGTCCTGTGTGTACAGAAGAAAGGAGAAAAAATTGCCCTTAACAGAAGAGTTGAGAAACAC
TGGCGTTTAATTGGTTGGGGTCAGATAAGAAGAGGAGTGACCATTAAGCCAACTGTAGATGATGAC

Alignment

ORF - retro_mmus_1408 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 88.47 %
• Parental protein coverage: 78.39 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  RSCGSSTPDEFPTDIPGTKGNFKLVRHVSFVDCPGHDILMATMLNGAAVMDAALLLIAGNESCPQPQTSE
          RSCGSSTPD.FPT.I.G.KGNFKLVRHVSFVDCPGHDILMATMLN.A..MDAALLLIA.NESCP.P...E
Retrocopy RSCGSSTPDKFPTYILGAKGNFKLVRHVSFVDCPGHDILMATMLNSAVEMDAALLLIASNESCPWP---E

Parental  HLAAIEIMKLKHILILQNKIDLVKESQAKEQYEQILAFVQGTVAE-GAPIIPISAQLKYNIEVVCEYIVK
          HL.A.EI.KLKHILILQNKIDLVKESQAKEQYEQ.LAFVQGT.AE.GAPIIPISAQLKYNIEVVCEYIVK
Retrocopy HLTAVEITKLKHILILQNKIDLVKESQAKEQYEQNLAFVQGTIAE>GAPIIPISAQLKYNIEVVCEYIVK

Parental  KIPVPPRDFTSEPRLIVIRSFDVNKPGCEVDDLKGGVAGGSILKGVLKVGQEIEVRPGIVSKDSEGKLMC
          KIPV.PRDFTSEP.LIVI...DVNKPGCEVDDLKGG.AGGSILKGVLKV.QEIEVRP.IVSKD.EGKLMC
Retrocopy KIPVAPRDFTSEPHLIVISPSDVNKPGCEVDDLKGGIAGGSILKGVLKVCQEIEVRPRIVSKDREGKLMC

Parental  KPIFSKIVSLF-AEHNDLQYAAPGGLIGVGTKIDPTLCRADRMVGQVLGAVGALPEIFTELEISYFLLRR
          KP.FS.IVSLF...HNDLQYAAPGGL.GVGTKI.PT.C.A.RMVGQVLGAVGALPEIFTELEISYFLL.R
Retrocopy KPTFSNIVSLFWGKHNDLQYAAPGGLTGVGTKIGPTVC*AGRMVGQVLGAVGALPEIFTELEISYFLLKR

Parental  LLGVRTEGDKKAAKVQKLSKNEVLMVNIGSLSTGGRVSAVKADLGKIVLTNPVCTE-VGEKIALSRRVEK
          LLGVRTEGDKKAAKVQKLSKNEVLMVNIGSL.TGGRVSAVKADLGKIVLT.PVCTE..GEKIAL.RRVEK
Retrocopy LLGVRTEGDKKAAKVQKLSKNEVLMVNIGSLLTGGRVSAVKADLGKIVLTSPVCTE>KGEKIALNRRVEK

Parental  HWRLIGWGQIRRGVTIKPTVDDD
          HWRLIGWGQIRRGVTIKPTVDDD
Retrocopy HWRLIGWGQIRRGVTIKPTVDDD

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	0.02 RPM	14.09 RPM
SRP007412_cerebellum	0.04 RPM	11.98 RPM
SRP007412_heart	0.03 RPM	19.83 RPM
SRP007412_kidney	0.00 RPM	16.38 RPM
SRP007412_liver	0.00 RPM	15.54 RPM
SRP007412_testis	3.34 RPM	1.01 RPM

ChIP-Seq

RNA Polymerase II activity may be related with retro_mmus_1408 in 3 libraries

ENCODE library ID	Target	ChIP-Seq Peak coordinates
ENCFF001XVA	POLR2A	15:75968919..75969546
ENCFF001YIJ	POLR2A	15:75968816..75969583
ENCFF001YKA	POLR2A	15:75968806..75969862

EST

No EST(s) were mapped for retro_mmus_1408 retrocopy.

TSS

No TSS is located nearby retro_mmus_1408 retrocopy 5' end.

Lab

retro_mmus_1408 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_1408 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 8 parental genes, and 13 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000014337	1 retrocopy	retro_btau_1497,
Equus caballus	ENSECAG00000017343	1 retrocopy	retro_ecab_810,
Macaca mulatta	ENSMMUG00000006979	4 retrocopies	retro_mmul_1965, retro_mmul_2258, retro_mmul_473, retro_mmul_713,
Monodelphis domestica	ENSMODG00000007541	2 retrocopies	retro_mdom_1650, retro_mdom_732,
Mus musculus	ENSMUSG00000035150	2 retrocopies	retro_mmus_1408 , retro_mmus_3433,
Pongo abelii	ENSPPYG00000020194	1 retrocopy	retro_pabe_10,
Sus scrofa	ENSSSCG00000012178	1 retrocopy	retro_sscr_805,
Ictidomys tridecemlineatus	ENSSTOG00000007144	1 retrocopy	retro_itri_582,