RetrogeneDB ID: retro_mmus_2495

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 4:107327486..107328212(-)
• Located in intron of: ENSMUSG00000057375

Retrocopy information

• Ensembl ID: ENSMUSG00000082279
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Rfc5
• Ensembl ID: ENSMUSG00000029363
• Aliases: None
• Description: replication factor C (activator 1) 5 [Source:MGI Symbol;Acc:MGI:1919401]

Sequence

>retro_mmus_2495
GATATCGTTTGGGAGCCAGTCCTCAGCTTTGCCAGCACAAGGACAATCTTCAAGAAAGGGTTTAAGCTTGTGATCCTGGA
CAAAGCCGACGCCATGCCTCAGGATGCCCAGAATGCCTTGAGACGGGTGATTGAGAAGTTCACAGAAAACACCAGGTTTT
GCCTCCTCTGTAACTACCGGTCCAAGATCATCCCTGCCTTGCAGTCACGGTGCACGGGGTTCCGATTTGGCCCTCCGACA
CCCAAGCTCATGGTCCCTCAACTGGAACACGTAGTACAAGAAGAGAATGTAGATATAAGTGAAGATGGAATGAAGGCCCT
TGTCACTCTGTCCAGTGGGGACATGCGAAGGGCTTTGAACATCCTGCAGAGTACCAATATGGCCTTTGGGAAGGTGACAG
AGGAGACTGTCTACACGTGCACCGGACACCCACTCAAGACGGACATCGCCAATATACTGGACTGGATGCTCAATCAGGAC
TTCACCACCGCCTACAAAAATATCATGGAGCTGAAGACTCTGAAGGGCTTGGCGCTGCATGACATTCTGACCGAGGTTCA
CTTGTTTGTACACAGAGTTGACTTTCCATCTTCAGTTCGGATACACTTATTGACCAAAATGGCAGACATTGAGTACAGAC
TTTCTGTTGGCACCAGTGAGAAGATACAGCTGAGCTCCCTCATCGCCGCTTTTCAAGTCACCAGAGACCTGATAGTTGCA
GAGGCC

Alignment

ORF - retro_mmus_2495 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 95.45 %
• Parental protein coverage: 71.39 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  DIVRGPILSFASTRTIFKKGFKLVILDEADAMTQDAQNALRRVIEKFTENTRFCLICNYLSKIIPALQSR
          DIV..P.LSFASTRTIFKKGFKLVILD.ADAM.QDAQNALRRVIEKFTENTRFCL.CNY.SKIIPALQSR
Retrocopy DIVWEPVLSFASTRTIFKKGFKLVILDKADAMPQDAQNALRRVIEKFTENTRFCLLCNYRSKIIPALQSR

Parental  CTRFRFGPLTPELMVPRLEHVVQEENVDISEDGMKALVTLSSGDMRRALNILQSTNMAFGKVTEETVYTC
          CT.FRFGP.TP.LMVP.LEHVVQEENVDISEDGMKALVTLSSGDMRRALNILQSTNMAFGKVTEETVYTC
Retrocopy CTGFRFGPPTPKLMVPQLEHVVQEENVDISEDGMKALVTLSSGDMRRALNILQSTNMAFGKVTEETVYTC

Parental  TGHPLKTDIANILDWMLNQDFTTAYKNIMELKTLKGLALHDILTEVHLFVHRVDFPSSVRIHLLTKMADI
          TGHPLKTDIANILDWMLNQDFTTAYKNIMELKTLKGLALHDILTEVHLFVHRVDFPSSVRIHLLTKMADI
Retrocopy TGHPLKTDIANILDWMLNQDFTTAYKNIMELKTLKGLALHDILTEVHLFVHRVDFPSSVRIHLLTKMADI

Parental  EYRLSVGTSEKIQLSSLIAAFQVTRDLIVAEA
          EYRLSVGTSEKIQLSSLIAAFQVTRDLIVAEA
Retrocopy EYRLSVGTSEKIQLSSLIAAFQVTRDLIVAEA

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	9.23 RPM
SRP007412_cerebellum	0.00 RPM	5.82 RPM
SRP007412_heart	0.03 RPM	2.96 RPM
SRP007412_kidney	0.08 RPM	5.85 RPM
SRP007412_liver	0.08 RPM	5.46 RPM
SRP007412_testis	0.09 RPM	3.38 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_2495 was not detected

EST

No EST(s) were mapped for retro_mmus_2495 retrocopy.

TSS

No TSS is located nearby retro_mmus_2495 retrocopy 5' end.

Lab

retro_mmus_2495 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_2495 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 4 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Equus caballus	ENSECAG00000015326	2 retrocopies	retro_ecab_613, retro_ecab_946,
Mus musculus	ENSMUSG00000029363	1 retrocopy	retro_mmus_2495 ,
Oryctolagus cuniculus	ENSOCUG00000010377	1 retrocopy	retro_ocun_1316,
Rattus norvegicus	ENSRNOG00000001134	1 retrocopy	retro_rnor_1139,