RetrogeneDB ID: retro_mmus_1648

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 17:56014279..56014555(-)
• Located in intron of: ENSMUSG00000003199

Retrocopy information

• Ensembl ID: ENSMUSG00000084755
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Bola3
• Ensembl ID: ENSMUSG00000045160
• Aliases: None
• Description: bolA-like 3 (E. coli) [Source:MGI Symbol;Acc:MGI:1925903]

Sequence

>retro_mmus_1648
GGGGCCCGGCGGTGGCACTGTGCGCAGCGAATGTTTGCCTCCCAGATGGAAGGGGAACTCAAAGTGACCCAGGTTCTCAA
AGAAAAGTTCCCTCGAGCTACAGCTCTTCAAGTCACAGACATCTCAGGAGGCTGCGGGGCGATGTATGAAATTAGAATCG
AATCAGAATTTAAAGAGAAGAGGACTGTCCAGCAGCACCAGATGGTCAATCAGGTATTAAAAGAAGAGATCAAGGGCATG
CACGGCCTACGGATATTCACCTCTGTCCCCAAGTGC

Alignment

ORF - retro_mmus_1648 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 91.4 %
• Parental protein coverage: 97.89 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  GLPLWHCAQRMFASQTEGELKVTQVLKEKFPRATAIQVTDISGGCGAMYEIKIESEEFKEKRTVQQHQMV
          G...WHCAQRMFASQ.EGELKVTQVLKEKFPRATA.QVTDISGGCGAMYEI.IES.EFKEKRTVQQHQMV
Retrocopy GARRWHCAQRMFASQMEGELKVTQVLKEKFPRATALQVTDISGGCGAMYEIRIES-EFKEKRTVQQHQMV

Parental  NQALKEEIKGMHGLRIFTSVPKC
          NQ.LKEEIKGMHGLRIFTSVPKC
Retrocopy NQVLKEEIKGMHGLRIFTSVPKC

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	0.30 RPM	10.37 RPM
SRP007412_cerebellum	0.48 RPM	22.06 RPM
SRP007412_heart	0.09 RPM	78.04 RPM
SRP007412_kidney	0.10 RPM	54.05 RPM
SRP007412_liver	0.38 RPM	33.32 RPM
SRP007412_testis	0.05 RPM	34.30 RPM

ChIP-Seq

RNA Polymerase II actvity may be related with retro_mmus_1648 in 2 libraries

ENCODE library ID	Target	ChIP-Seq Peak coordinates
ENCFF001YIJ	POLR2A	17:56015351..56015429
ENCFF001YKA	POLR2A	17:56015504..56015766
ENCFF001YKA	POLR2A	17:56015059..56015083

EST

No EST(s) were mapped for retro_mmus_1648 retrocopy.

TSS

No TSS is located nearby retro_mmus_1648 retrocopy 5' end.

Lab

retro_mmus_1648 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_1648 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 17 parental genes, and 32 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000008739	1 retrocopy	retro_cfam_1574,
Callithrix jacchus	ENSCJAG00000017844	1 retrocopy	retro_cjac_1112,
Dasypus novemcinctus	ENSDNOG00000008309	2 retrocopies	retro_dnov_2474, retro_dnov_510,
Homo sapiens	ENSG00000163170	3 retrocopies	retro_hsap_1959, retro_hsap_3383, retro_hsap_4148,
Gorilla gorilla	ENSGGOG00000024505	4 retrocopies	retro_ggor_1423, retro_ggor_1424, retro_ggor_2290, retro_ggor_2786,
Myotis lucifugus	ENSMLUG00000016364	1 retrocopy	retro_mluc_1407,
Macaca mulatta	ENSMMUG00000015207	2 retrocopies	retro_mmul_1181, retro_mmul_2109,
Mustela putorius furo	ENSMPUG00000007813	1 retrocopy	retro_mputfur_1519,
Mus musculus	ENSMUSG00000045160	1 retrocopy	retro_mmus_1648 ,
Nomascus leucogenys	ENSNLEG00000000320	4 retrocopies	retro_nleu_1391, retro_nleu_1567, retro_nleu_2604, retro_nleu_971,
Oryctolagus cuniculus	ENSOCUG00000016658	1 retrocopy	retro_ocun_51,
Otolemur garnettii	ENSOGAG00000003502	1 retrocopy	retro_ogar_1839,
Pongo abelii	ENSPPYG00000012285	2 retrocopies	retro_pabe_1618, retro_pabe_3461,
Pan troglodytes	ENSPTRG00000012078	3 retrocopies	retro_ptro_1309, retro_ptro_2299, retro_ptro_2820,
Sorex araneus	ENSSARG00000001754	1 retrocopy	retro_sara_83,
Sus scrofa	ENSSSCG00000008291	1 retrocopy	retro_sscr_750,
Tursiops truncatus	ENSTTRG00000006698	3 retrocopies	retro_ttru_1149, retro_ttru_1493, retro_ttru_254,