RetrogeneDB ID: retro_rnor_2614

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 8:26304088..26304556(-)
• Located in intron of: ENSRNOG00000029995

Retrocopy information

• Ensembl ID: ENSRNOG00000043330
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Chmp5
• Ensembl ID: ENSRNOG00000008672
• Aliases: Chmp5, RGD1305968
• Description: Charged multivesicular body protein 5 [Source:UniProtKB/Swiss-Prot;Acc:Q4QQV8]

Sequence

>retro_rnor_2614
ATGAACCGATTCTTTGGAAAGCAAAACCCAAGGCTCCGCCACCTAGCCTGACTGCATTGGGACGGTGGATAGCAGGGCAG
GATCCATTCACAAAAAGTTTCCAGGTTGGATGCTGAACTAGTGAGGTATAAGGATCAGCTCAAGAAGATGAGAGAGGGTC
CTGCTAAGAACATGGTCGAACAGAAAGCTCTGAGGGTTTTGAAGCAAAAGTGGATGTTTGAGCGAGACACCCTTGCCCAA
CAGTTCTTTAATATGGAGCAAGCTAATTACACCATCCAGTCACTGGAGGACAGCAGGACCGTGGTTGATGCCATGAAATT
AGGAGTAAAGGGAATGAGGAAGGCTTACAAGGAAGTCAGAGTCGACCAGATTGAGGATATACAAGGCCAGCTGGAAGACA
TGGTGGAAGATGCAAACGGGACCCAGGAAGCCCTGGGCCGCACCTACGGCACCCCAGAACTAGATGAG

Alignment

ORF - retro_rnor_2614 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 79.75 %
• Parental protein coverage: 73.06 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  MNRFFGK-AKPKAPPPSLT-DCIGTVDSRAESIDKK-ISRLDAELVKYKDQIKKMREGPAKNMVKQKALR
          MNRFFGK.AKPKA.PP....DCIGTVDSRA.SI.KK..SRLDAELV.YKDQ.KKMREGPAKNMV.QKALR
Retrocopy MNRFFGK<AKPKA-PPPSL<DCIGTVDSRAGSIHKK<VSRLDAELVRYKDQLKKMREGPAKNMVEQKALR

Parental  VLKQKRMYEQQRDNLAQQSFNMEQANYTIQSLKDTKTTVDAMKLGVKEMKKAYKEVKIDQIEDLQDQLED
          VLKQK.M.E..RD.LAQQ.FNMEQANYTIQSL.D..T.VDAMKLGVK.M.KAYKEV..DQIED.Q.QLED
Retrocopy VLKQKWMFE--RDTLAQQFFNMEQANYTIQSLEDSRTVVDAMKLGVKGMRKAYKEVRVDQIEDIQGQLED

Parental  MMEDANEIQEALGRSYGTPELDE
          M.EDAN..QEALGR.YGTPELDE
Retrocopy MVEDANGTQEALGRTYGTPELDE

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
SRP017611_brain	0.07 RPM	59.46 RPM
SRP017611_kidney	0.00 RPM	78.16 RPM
SRP017611_liver	0.07 RPM	31.74 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_2614 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_2614 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_2614 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

Parental genes homology involve 19 parental genes, and 37 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000012672	1 retrocopy	retro_chof_2045,
Callithrix jacchus	ENSCJAG00000008104	2 retrocopies	retro_cjac_2868, retro_cjac_4159,
Cavia porcellus	ENSCPOG00000003467	2 retrocopies	retro_cpor_1221, retro_cpor_1306,
Dipodomys ordii	ENSDORG00000006280	2 retrocopies	retro_dord_292, retro_dord_764,
Echinops telfairi	ENSETEG00000001424	1 retrocopy	retro_etel_2126,
Homo sapiens	ENSG00000086065	2 retrocopies	retro_hsap_4822, retro_hsap_494,
Microcebus murinus	ENSMICG00000012113	2 retrocopies	retro_mmur_369, retro_mmur_843,
Myotis lucifugus	ENSMLUG00000011045	1 retrocopy	retro_mluc_954,
Macaca mulatta	ENSMMUG00000020149	1 retrocopy	retro_mmul_2573,
Monodelphis domestica	ENSMODG00000004012	2 retrocopies	retro_mdom_2002, retro_mdom_595,
Mus musculus	ENSMUSG00000028419	1 retrocopy	retro_mmus_1469,
Nomascus leucogenys	ENSNLEG00000005158	2 retrocopies	retro_nleu_2197, retro_nleu_2420,
Otolemur garnettii	ENSOGAG00000000774	6 retrocopies	retro_ogar_2072, retro_ogar_2190, retro_ogar_2386, retro_ogar_2504, retro_ogar_2509, retro_ogar_916,
Pongo abelii	ENSPPYG00000019137	2 retrocopies	retro_pabe_239, retro_pabe_3750,
Pan troglodytes	ENSPTRG00000020857	2 retrocopies	retro_ptro_3210, retro_ptro_373,
Rattus norvegicus	ENSRNOG00000008672	1 retrocopy	retro_rnor_2614 ,
Ictidomys tridecemlineatus	ENSSTOG00000026573	1 retrocopy	retro_itri_424,
Tupaia belangeri	ENSTBEG00000003486	5 retrocopies	retro_tbel_1626, retro_tbel_1894, retro_tbel_2407, retro_tbel_3364, retro_tbel_3494,
Tursiops truncatus	ENSTTRG00000010575	1 retrocopy	retro_ttru_338,