RetrogeneDB ID: retro_mmus_2996

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 7:12085924..12086576(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMUSG00000066807
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Rnf141
• Ensembl ID: ENSMUSG00000030788
• Aliases: None
• Description: ring finger protein 141 [Source:MGI Symbol;Acc:MGI:1914400]

Sequence

>retro_mmus_2996
ATTAACAAGTTACCAGAAAAGGTAGCAAAGCACGTCACCTTGGTTCGAGAAAGTGGCTCCTTAACTTACGAAGAGTTTCT
TGGGAGAGTAGCTGAACTCAATGATGTAACTGCTAAGGTGGCTGCTGGCCAGGAAAAGCATCTTCTCTTTGAGGTACAAC
CTGGGTCTGACTCCTCTGCCTTCTGGAAAGTGGTTGTACGGGTGGTCTGTACCAAGATTAACAAAAGGTGGCATTGTGGA
AGCATCGCGGATCATGAATTTGTACCAGTTTATTCAGCTCTATAAAGACATCACAAGCCAAGCTGCTGGAGTGCTGGCTC
AGAGCTCCACCTCTGAAGAGCCTGATGGCAACCCATCCTCGGTCACATCTTGCCAGGCTAGTCTATGGATGGGCAGGGTG
AAGCAGCTGACTGATGAGGAGGAGTGTTGTATCTGCATGGACGGGCGAGCTGACCTCATCCTGCCCTGTGCTCACAGCTT
CTGTCAGAAGTGCATTGATAAATGGAGTGATCGACACAGGAACTGCCCCATTTGTCGCCTACAGATGACTGGAGCAAATG
AATCATGGGTGGTGTCAGATGCACCCACTGAAGATGACATGGCTAACTATATTCTTAACATGGCTGATGAGGCAGGCCAG
CCCCACAGGCCA

Alignment

ORF - retro_mmus_2996 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 96.8 %
• Parental protein coverage: 94.78 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  INKLPEKVAKHVTLVRESGSLTYEEFLGRVAELNDVTAKVAAGQEKHLLFEVQPGSDSSAFWKVVVRVVC
          INKLPEKVAKHVTLVRESGSLTYEEFLGRVAELNDVTAKVAAGQEKHLLFEVQPGSDSSAFWKVVVRVVC
Retrocopy INKLPEKVAKHVTLVRESGSLTYEEFLGRVAELNDVTAKVAAGQEKHLLFEVQPGSDSSAFWKVVVRVVC

Parental  T-KINKSSGIVEASRIMNLYQFIQLYKDITSQAAGVLAQSSTSEEPDENPSSVTSCQASLWMGRVKQLTD
          T....K..GIVEASRIMNLYQFIQLYKDITSQAAGVLAQSSTSEEPD.NPSSVTSCQASLWMGRVKQLTD
Retrocopy T>RLTKG-GIVEASRIMNLYQFIQLYKDITSQAAGVLAQSSTSEEPDGNPSSVTSCQASLWMGRVKQLTD

Parental  EEECCICMDGRADLILPCAHSFCQKCIDKWSDRHRNCPICRLQMTGANESWVVSDAPTEDDMANYILNMA
          EEECCICMDGRADLILPCAHSFCQKCIDKWSDRHRNCPICRLQMTGANESWVVSDAPTEDDMANYILNMA
Retrocopy EEECCICMDGRADLILPCAHSFCQKCIDKWSDRHRNCPICRLQMTGANESWVVSDAPTEDDMANYILNMA

Parental  DEAGQPHRP
          DEAGQPHRP
Retrocopy DEAGQPHRP

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	0.33 RPM	59.01 RPM
SRP007412_cerebellum	0.69 RPM	36.95 RPM
SRP007412_heart	0.03 RPM	23.50 RPM
SRP007412_kidney	0.73 RPM	25.04 RPM
SRP007412_liver	0.79 RPM	34.05 RPM
SRP007412_testis	7.27 RPM	34.62 RPM

ChIP-Seq

RNA Polymerase II activity near the 5' end of retro_mmus_2996 was not detected

EST

No EST(s) were mapped for retro_mmus_2996 retrocopy.

TSS

No TSS is located nearby retro_mmus_2996 retrocopy 5' end.

Lab

retro_mmus_2996 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_2996 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 8 parental genes, and 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000011014	1 retrocopy	retro_cjac_3999,
Cavia porcellus	ENSCPOG00000007808	2 retrocopies	retro_cpor_175, retro_cpor_198,
Macropus eugenii	ENSMEUG00000014558	1 retrocopy	retro_meug_1251,
Mus musculus	ENSMUSG00000030788	1 retrocopy	retro_mmus_2996 ,
Oryctolagus cuniculus	ENSOCUG00000002807	1 retrocopy	retro_ocun_1507,
Otolemur garnettii	ENSOGAG00000001765	1 retrocopy	retro_ogar_1262,
Sarcophilus harrisii	ENSSHAG00000002101	2 retrocopies	retro_shar_148, retro_shar_694,
Ictidomys tridecemlineatus	ENSSTOG00000019740	1 retrocopy	retro_itri_1573,