RetrogeneDB ID: retro_mmus_1984

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 2:149356916..149357402(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMUSG00000081470
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Clns1a
• Ensembl ID: ENSMUSG00000025439
• Aliases: None
• Description: chloride channel, nucleotide-sensitive, 1A [Source:MGI Symbol;Acc:MGI:109638]

Sequence

>retro_mmus_1984
CAAGAACATTTGTGTGTTATGGTGAATGCCAAGCTTGGAGAAGAATCAAAAGAACCTCTCTCTGATGAAGATGAGGAAGA
CAATGATGATGTTGAACCCATTTCTGAATTTAGATTTGCGCCCAGTGATAAGTCAGCCTTGGAGGCGATGTTCACAGCAA
TGTGTGAGTGCCAGGCCTTGCATCCAGACCCTGAGGATAAAGACTCAGATGACTATGATGGAGAGGAATATGACGTGGAG
GCACACGAACAAGAACAAGGAGACATCCCTACATTTTATACCTATGAAGAAGGACTATCCCATTTAACAGCGGAAGGGCA
AGCCACATTGGAGAGATTAGAGGGGATGCTTTCTCAGTCTGTGAGCAGCCAATATAATATGGCAGGCATCCGAACAGAAG
ATTCAGTAAGAAATTATGAAGATGGCATGGAGGTAGAAACCACACCAACTCTTGCCGGACAGTTTGAGGATGCAGATGCT
GATCAC

Alignment

ORF - retro_mmus_1984 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 95.68 %
• Parental protein coverage: 67.22 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  QEHLYVMVNAKLGEESKEPLSDEDEEDNDDVEPISEFRFVPSDKSALEAMFTAMCECQALHPDPEDEDSD
          QEHL.VMVNAKLGEESKEPLSDEDEEDNDDVEPISEFRF.PSDKSALEAMFTAMCECQALHPDPED.DSD
Retrocopy QEHLCVMVNAKLGEESKEPLSDEDEEDNDDVEPISEFRFAPSDKSALEAMFTAMCECQALHPDPEDKDSD

Parental  DYDGEEYDVEAHEQGQGDIPTFYTYEEGLSHLTAEGQATLERLEGMLSQSVSSQYNMAGVRTEDSVRNYE
          DYDGEEYDVEAHEQ.QGDIPTFYTYEEGLSHLTAEGQATLERLEGMLSQSVSSQYNMAG.RTEDSVRNYE
Retrocopy DYDGEEYDVEAHEQEQGDIPTFYTYEEGLSHLTAEGQATLERLEGMLSQSVSSQYNMAGIRTEDSVRNYE

Parental  DGMEVETTPTVAGQFEDADVDH
          DGMEVETTPT.AGQFEDAD.DH
Retrocopy DGMEVETTPTLAGQFEDADADH

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	0.02 RPM	48.06 RPM
SRP007412_cerebellum	0.04 RPM	42.38 RPM
SRP007412_heart	0.03 RPM	19.64 RPM
SRP007412_kidney	0.00 RPM	24.29 RPM
SRP007412_liver	0.08 RPM	23.35 RPM
SRP007412_testis	0.05 RPM	26.35 RPM

ChIP-Seq

RNA Polymerase II activity near the 5' end of retro_mmus_1984 was not detected

EST

No EST(s) were mapped for retro_mmus_1984 retrocopy.

TSS

No TSS is located nearby retro_mmus_1984 retrocopy 5' end.

Lab

retro_mmus_1984 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_1984 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 14 parental genes, and 27 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000019930	1 retrocopy	retro_btau_376,
Canis familiaris	ENSCAFG00000004900	6 retrocopies	retro_cfam_1112, retro_cfam_1448, retro_cfam_255, retro_cfam_327, retro_cfam_720, retro_cfam_727,
Callithrix jacchus	ENSCJAG00000014927	1 retrocopy	retro_cjac_4085,
Cavia porcellus	ENSCPOG00000005260	1 retrocopy	retro_cpor_67,
Felis catus	ENSFCAG00000026321	1 retrocopy	retro_fcat_736,
Homo sapiens	ENSG00000074201	2 retrocopies	retro_hsap_3010, retro_hsap_3595,
Gorilla gorilla	ENSGGOG00000003091	1 retrocopy	retro_ggor_2084,
Macropus eugenii	ENSMEUG00000005935	4 retrocopies	retro_meug_1825, retro_meug_2097, retro_meug_783, retro_meug_929,
Mus musculus	ENSMUSG00000025439	1 retrocopy	retro_mmus_1984 ,
Nomascus leucogenys	ENSNLEG00000016699	2 retrocopies	retro_nleu_300, retro_nleu_756,
Oryctolagus cuniculus	ENSOCUG00000024393	1 retrocopy	retro_ocun_1303,
Pongo abelii	ENSPPYG00000003712	1 retrocopy	retro_pabe_2494,
Sorex araneus	ENSSARG00000009460	2 retrocopies	retro_sara_247, retro_sara_682,
Ictidomys tridecemlineatus	ENSSTOG00000027980	3 retrocopies	retro_itri_239, retro_itri_319, retro_itri_490,