RetrogeneDB ID: retro_mmus_2094

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 2:137747529..137747965(-)
• Located in intron of: ENSMUSG00000085640

Retrocopy information

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

Parental gene information

• Parental gene symbol: Chp1
• Ensembl ID: ENSMUSG00000014077
• Aliases: Chp1, 1500003O03Rik, AA960066, AI046351, Cahp, Chp, Sid470p, p24, vac
• Description: calcineurin-like EF hand protein 1 [Source:MGI Symbol;Acc:MGI:1927185]

Sequence

>retro_mmus_2094
GAGGCTGGAACTCTAAGCTTGGGAGGTTTCCAGATGATTCTAGAACTTGCCATAAACCCAGTGGGGGACAGCACAAGCAA
TGCCTTCATTTCAGAGGGTGAGGCCCAAGTGAGCTTCTGATTACTGATGAGAACTTTGACTCATTTCTGACCCATTGAGG
GACATAAAAACAAAACAAAACAACAACAACGAAAATCACTCAACTGCCAGAGGAAGAACCTGTACTTTGTTCTCAGATTA
TACAATATGAATAAAGATGACAAGCTCTCCTTTGATAAGCTGTTACAGATCTACAAATGACGGTTGGAGTAGAAATCTCT
GATGGGCAGCTGGGCATTGTCACAGACAGGACCATCCAGGAGGCAGCTCAGGCTGGGGATACTGACAAATTTTTGTAGAA
TTTGTTAAGGATTTATAAAAGGTGGGTGTAGAACAG

Alignment

ORF - retro_mmus_2094 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 52.7 %
• Parental protein coverage: 74.87 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  ENGTLSREDFQRIPELAINPLGDRIINAFFSEGEDQVNFRGFMRTLAHFRPIEDNEKSKDVNGPEPLNSR
          E.GTLS...FQ.I.ELAINP.GD...NAF.SEGE.QV.F...MRTL.HF.PIE.............LN..
Retrocopy EAGTLSLGGFQMILELAINPVGDSTSNAFISEGEAQVSF*LLMRTLTHF*PIEGHXXXXXXXXXXSLNCQ

Parental  SNKLHFAFRLYDLDKDDKISRDELLQV-LRMMVGVNISDEQLGSIADRTIQEADQDGDSAISFTEFVKV-
          ...L.F..RLY...KDDK.S.D.LLQ..L.M.VGV.ISD.QLG...DRTIQEA.Q.GD............
Retrocopy RKNLYFVLRLYNMNKDDKLSFDKLLQI<LQMTVGVEISDGQLGIVTDRTIQEAAQAGDTDKFL*NLLRI<

Parental  LEKVDVEQ
          L.KV.VEQ
Retrocopy L*KVGVEQ

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	107.07 RPM
SRP007412_cerebellum	0.00 RPM	72.47 RPM
SRP007412_heart	0.00 RPM	68.24 RPM
SRP007412_kidney	0.00 RPM	111.34 RPM
SRP007412_liver	0.00 RPM	243.29 RPM
SRP007412_testis	0.00 RPM	16.74 RPM

ChIP-Seq

RNA Polymerase II activity near the 5' end of retro_mmus_2094 was not detected

EST

No EST(s) were mapped for retro_mmus_2094 retrocopy.

TSS

No TSS is located nearby retro_mmus_2094 retrocopy 5' end.

Lab

retro_mmus_2094 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_2094 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 12 parental genes, and 25 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000009525	1 retrocopy	retro_cfam_2136,
Cavia porcellus	ENSCPOG00000010577	2 retrocopies	retro_cpor_1224, retro_cpor_726,
Homo sapiens	ENSG00000187446	2 retrocopies	retro_hsap_3334, retro_hsap_3541,
Gorilla gorilla	ENSGGOG00000007312	2 retrocopies	retro_ggor_1293, retro_ggor_2392,
Macaca mulatta	ENSMMUG00000017092	2 retrocopies	retro_mmul_1809, retro_mmul_2088,
Mus musculus	ENSMUSG00000014077	4 retrocopies	retro_mmus_1458, retro_mmus_2094 , retro_mmus_3133, retro_mmus_3469,
Nomascus leucogenys	ENSNLEG00000003465	4 retrocopies	retro_nleu_1678, retro_nleu_2269, retro_nleu_2608, retro_nleu_2609,
Procavia capensis	ENSPCAG00000005419	1 retrocopy	retro_pcap_240,
Pongo abelii	ENSPPYG00000006370	2 retrocopies	retro_pabe_2749, retro_pabe_2925,
Pan troglodytes	ENSPTRG00000006942	2 retrocopies	retro_ptro_2144, retro_ptro_2407,
Rattus norvegicus	ENSRNOG00000004742	2 retrocopies	retro_rnor_2034, retro_rnor_2223,
Ictidomys tridecemlineatus	ENSSTOG00000014503	1 retrocopy	retro_itri_227,