RetrogeneDB ID: retro_mmus_702

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 11:31287399..31287681(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Snapc5
• Ensembl ID: ENSMUSG00000032398
• Aliases: Snapc5, 2010103A03Rik
• Description: small nuclear RNA activating complex, polypeptide 5 [Source:MGI Symbol;Acc:MGI:1914282]

Sequence

>retro_mmus_702
GAGATGGAAGAAGAGCTGCACAAGGTAGCCATGCCTAAAGGTGGCTTGTATGACCAACTGAACCACCTCAAGGTTGAAGA
ATAGGACCTCTAATCAATGATAAATTTTCAAGGAGGGACTGAAACACTGTCTTATCAGTCTGCACCTGAATAGTTATGTG
ATATGTCACTGCATGTAGACAATGAATGTTCATCGATTAAACCACTGAAGCTGAGCACAAGAAGCCATAGGGAGGAAGAG
CAGGAAGAGGAGGAGGTGGTAAAGGAGGAAGAATCTGATTCA

Alignment

ORF - retro_mmus_702 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 61.46 %
• Parental protein coverage: 94.12 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  ELRKEEETLLRLKAALHDQLNRLKVEELALQSMINSRGRTETLSSQPAPEQLCDMSLHVDNEVTINQTTL
          E...E.......K..L.DQLN.LKVEE..L.SMIN..G.TETLS.Q.APE.LCDMSLHVDNE.......L
Retrocopy EMEEELHKVAMPKGGLYDQLNHLKVEE*DL*SMINFQGGTETLSYQSAPE*LCDMSLHVDNECS-SIKPL

Parental  KLSTRSPMEEEEEEEEEEEEEEESDS
          KLSTRS...EEE.EEEE...EEESDS
Retrocopy KLSTRS-HREEEQEEEEVVKEEESDS

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	0.00 RPM	15.58 RPM
SRP007412_cerebellum	0.00 RPM	12.55 RPM
SRP007412_heart	0.00 RPM	17.18 RPM
SRP007412_kidney	0.00 RPM	18.75 RPM
SRP007412_liver	0.00 RPM	10.10 RPM
SRP007412_testis	0.00 RPM	12.62 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_702 was not detected

EST

No EST(s) were mapped for retro_mmus_702 retrocopy.

TSS

No TSS is located nearby retro_mmus_702 retrocopy 5' end.

Lab

retro_mmus_702 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_702 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Rattus norvegicus	retro_rnor_1087

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Parental genes homology:

Parental genes homology involve 12 parental genes, and 12 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000017304	1 retrocopy	retro_cfam_1063,
Callithrix jacchus	ENSCJAG00000007484	1 retrocopy	retro_cjac_2314,
Dasypus novemcinctus	ENSDNOG00000006689	1 retrocopy	retro_dnov_1203,
Gorilla gorilla	ENSGGOG00000003693	1 retrocopy	retro_ggor_2398,
Macropus eugenii	ENSMEUG00000003990	1 retrocopy	retro_meug_1590,
Macaca mulatta	ENSMMUG00000016841	1 retrocopy	retro_mmul_1815,
Mus musculus	ENSMUSG00000032398	1 retrocopy	retro_mmus_702 ,
Nomascus leucogenys	ENSNLEG00000012935	1 retrocopy	retro_nleu_2325,
Oryctolagus cuniculus	ENSOCUG00000008791	1 retrocopy	retro_ocun_1059,
Rattus norvegicus	ENSRNOG00000010156	1 retrocopy	retro_rnor_1087,
Ictidomys tridecemlineatus	ENSSTOG00000009201	1 retrocopy	retro_itri_1582,
Tupaia belangeri	ENSTBEG00000014333	1 retrocopy	retro_tbel_68,