RetrogeneDB ID: retro_mmus_1267

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 14:45557642..45558173(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Gid8
• Ensembl ID: ENSMUSG00000027573
• Aliases: Gid8, 2310003C23Rik, 4833420G11Rik, AI451474, Twa1
• Description: GID complex subunit 8 homolog (S. cerevisiae) [Source:MGI Symbol;Acc:MGI:1923675]

Sequence

>retro_mmus_1267
ATGAGTTATGCAGAAAAGCCGGATGAAATAACCAAAGATGAATGGATGGGAAAGCTCAATAACTTGCATGTTCAGCGAGC
AGACATGAACCAACTCATGAACTACCTAGTCACAGAGGGCTTTAAGGAAGCAACAGAGAAATTTCGGATGGAGTCTGGGA
TGAAACCAAGTGTGGACCTAGAAACATTTGATGAGCGAATCAAGATTCGGGAGATGATTCTGAAGGGTCAGATCCAGGCG
GCCATCGCCTTGATCAACAGCCTCCACCCAGAGCTCCTAGACACAAACCGGTATCTTTACTTCCACCTTCAGCAACAACA
CTTGATTGAGCTTATCTGTCAGCGTGAGACAGAAGCAGCATTGGCGTTTGCCCAGACGCAACTGGCAGAGCAGGGTGAGG
AAAGCCGAGAATGCCTCACAGAGATGGAGCGCACACTGGCCTTGCTGGCCTTCGATAGCCCTGAGGAGTCGACTTTTGGA
GACCTCCTCCACATGATGCAGAGGCAAAAGGTATGGAGTGACGTTAACCAG

Alignment

ORF - retro_mmus_1267 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 93.26 %
• Parental protein coverage: 78.07 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MSYAEKPDEITKDEWMEKLNNLHVQRADMNRLIMNYLVTEGFKEAAEKFRMESGIEPSVDLETLDERIKI
          MSYAEKPDEITKDEWM.KLNNLHVQRADMN.L.MNYLVTEGFKEA.EKFRMESG..PSVDLET.DERIKI
Retrocopy MSYAEKPDEITKDEWMGKLNNLHVQRADMNQL-MNYLVTEGFKEATEKFRMESGMKPSVDLETFDERIKI

Parental  REMILKGQIQEAIALINSLHPELLDTNRYLYFHLQQQHLIELIRQRETEAALEFAQTQLAEQGEESRECL
          REMILKGQIQ.AIALINSLHPELLDTNRYLYFHLQQQHLIELI.QRETEAAL.FAQTQLAEQGEESRECL
Retrocopy REMILKGQIQAAIALINSLHPELLDTNRYLYFHLQQQHLIELICQRETEAALAFAQTQLAEQGEESRECL

Parental  TEMERTLALLAFDSPEESPFGDLLHMMQRQKVWSEVNQ
          TEMERTLALLAFDSPEES.FGDLLHMMQRQKVWS.VNQ
Retrocopy TEMERTLALLAFDSPEESTFGDLLHMMQRQKVWSDVNQ

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	0.05 RPM	30.35 RPM
SRP007412_cerebellum	0.00 RPM	30.26 RPM
SRP007412_heart	0.00 RPM	33.56 RPM
SRP007412_kidney	0.00 RPM	29.68 RPM
SRP007412_liver	0.05 RPM	27.96 RPM
SRP007412_testis	0.32 RPM	29.82 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_1267 was not detected

EST

No EST(s) were mapped for retro_mmus_1267 retrocopy.

TSS

No TSS is located nearby retro_mmus_1267 retrocopy 5' end.

Lab

retro_mmus_1267 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_1267 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 7 parental genes, and 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000012749	1 retrocopy	retro_cfam_1551,
Myotis lucifugus	ENSMLUG00000016381	2 retrocopies	retro_mluc_417, retro_mluc_418,
Monodelphis domestica	ENSMODG00000016835	1 retrocopy	retro_mdom_1208,
Mus musculus	ENSMUSG00000027573	1 retrocopy	retro_mmus_1267 ,
Otolemur garnettii	ENSOGAG00000013834	1 retrocopy	retro_ogar_2550,
Rattus norvegicus	ENSRNOG00000010180	1 retrocopy	retro_rnor_2248,
Sorex araneus	ENSSARG00000013102	2 retrocopies	retro_sara_396, retro_sara_598,