RetrogeneDB ID: retro_mmus_2121

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 2:162919273..162919684(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Cisd3
• Ensembl ID: ENSMUSG00000078695
• Aliases: Cisd3, Mel-13, Mel13
• Description: CDGSH iron sulfur domain 3 [Source:MGI Symbol;Acc:MGI:101788]

Sequence

>retro_mmus_2121
ATGGGCTTCCGGCGTCTCTCCTTCCCCACTGATTTTATTTTTCTGTTTCCAAATCATATCTGCCTGCCTGCCTTGTCGAA
GCCGTATCAGAGGCGGGAAATCTCTTCTTGGCTGGCCCGATGGTTCCCCAAAGAGCCAACCAAGCCAGTGGTGGCACAGA
AGACACACATCAGATTGGAGCTGGTTGCTGGGAAAAACTACAGGTGGTGTGTATGTGGCCGAAGCAAGAATCAGCCCTTC
TGTGATGGCTCCCACTTCTTCCAGCGTACTGGCCTTTCTCCACTCAAGTTCAAGGTCCAAGAGACACGCACAGTGGCCCT
ATGTACCTGCAAGGCCACTCGGCGGCCCCCTTACTGTGACGGTACCCACAAGAGTGAGCAGGTACAGAAAGCAGAAGTAG
GTTCCCCACTC

Alignment

ORF - retro_mmus_2121 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 95.62 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MGFRRLSFPTDFIFLFPNHICLPALSKPYQRREISSWLARWFPKDPAKPVVAQKTPIRLELVAGKTYRWC
          MGFRRLSFPTDFIFLFPNHICLPALSKPYQRREISSWLARWFPK.P.KPVVAQKT.IRLELVAGK.YRWC
Retrocopy MGFRRLSFPTDFIFLFPNHICLPALSKPYQRREISSWLARWFPKEPTKPVVAQKTHIRLELVAGKNYRWC

Parental  VCGRSKNQPFCDGSHFFQRTGLSPLKFKAQETRTVALCTCKATQRPPYCDGTHKSEQVQKAEVGSPL
          VCGRSKNQPFCDGSHFFQRTGLSPLKFK.QETRTVALCTCKAT.RPPYCDGTHKSEQVQKAEVGSPL
Retrocopy VCGRSKNQPFCDGSHFFQRTGLSPLKFKVQETRTVALCTCKATRRPPYCDGTHKSEQVQKAEVGSPL

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	6.47 RPM
SRP007412_cerebellum	0.00 RPM	5.78 RPM
SRP007412_heart	0.00 RPM	20.48 RPM
SRP007412_kidney	0.13 RPM	15.63 RPM
SRP007412_liver	0.03 RPM	14.47 RPM
SRP007412_testis	0.00 RPM	2.15 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_2121 was not detected

EST

No EST(s) were mapped for retro_mmus_2121 retrocopy.

TSS

No TSS is located nearby retro_mmus_2121 retrocopy 5' end.

Lab

retro_mmus_2121 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_2121 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 2 parental genes, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000046569	1 retrocopy	retro_btau_1227,
Mus musculus	ENSMUSG00000078695	1 retrocopy	retro_mmus_2121 ,