RetrogeneDB ID: retro_mmus_778

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 11:30822314..30822670(-)
• Located in intron of: ENSMUSG00000040850

Retrocopy information

• Ensembl ID: ENSMUSG00000086986
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Ska2
• Ensembl ID: ENSMUSG00000020492
• Aliases: None
• Description: spindle and kinetochore associated complex subunit 2 [Source:MGI Symbol;Acc:MGI:1913390]

Sequence

>retro_mmus_778
ATGGTGGCGGAGGTCAATAAACTGGAACTGATGGTCCAGAAAGCTGACTCTGATTTGGACTACCTTCAATATAGGCTGGA
ATATGAAATCAAAACTAATCACCCTCATTCAGCAGGACAGAAAAATGCAGTTGCAATTTTAAAGGAATTATCAGCAATAA
GGTCTCAATATCAAGCTTTATATGCAGCTTTAAGGCAGTTTCTGTTGAGCAAAGAGACCAAGAGCTGCATTTGTGGTATT
TTGAACAAGACAATGACCATGATACAAGAACTACAAAAGCAAACAAACCTGGAGCTTACTCTACTGACTGAAGAAGAGAA
AGCTGTGACAGAGCAATTAAGTCTCACATGCCAGAC

Alignment

ORF - retro_mmus_778 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 80.17 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MEAEVDKLELMFQKADSDLDYLQYRLEYEVKTNHPHSAGEKNAVTVLKELSAIKSRYQALCARFKAVSVE
          M.AEV.KLELM.QKADSDLDYLQYRLEYE.KTNHPHSAG.KNAV..LKELSAI.S.YQAL.A........
Retrocopy MVAEVNKLELMVQKADSDLDYLQYRLEYEIKTNHPHSAGQKNAVAILKELSAIRSQYQALYAALRQFLLS

Parental  QKETKSCICATLNKTMTMIQELQKQTNLELTLLTEEEKAATEPL-KSHMPD
          .KETKSCIC..LNKTMTMIQELQKQTNLELTLLTEEEKA.TE.L.KSHMPD
Retrocopy -KETKSCICGILNKTMTMIQELQKQTNLELTLLTEEEKAVTEQL<KSHMPD

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	0.14 RPM	8.53 RPM
SRP007412_cerebellum	0.04 RPM	8.90 RPM
SRP007412_heart	0.03 RPM	9.68 RPM
SRP007412_kidney	0.00 RPM	7.53 RPM
SRP007412_liver	0.00 RPM	1.09 RPM
SRP007412_testis	0.14 RPM	5.40 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_778 was not detected

EST

No EST(s) were mapped for retro_mmus_778 retrocopy.

TSS

No TSS is located nearby retro_mmus_778 retrocopy 5' end.

Lab

retro_mmus_778 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_778 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 18 parental genes, and 32 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000021680	2 retrocopies	retro_btau_310, retro_btau_945,
Canis familiaris	ENSCAFG00000029233	1 retrocopy	retro_cfam_766,
Cavia porcellus	ENSCPOG00000006051	1 retrocopy	retro_cpor_542,
Dipodomys ordii	ENSDORG00000010768	2 retrocopies	retro_dord_103, retro_dord_281,
Equus caballus	ENSECAG00000015007	1 retrocopy	retro_ecab_987,
Felis catus	ENSFCAG00000022802	1 retrocopy	retro_fcat_1111,
Homo sapiens	ENSG00000182628	1 retrocopy	retro_hsap_4214,
Loxodonta africana	ENSLAFG00000003405	1 retrocopy	retro_lafr_1215,
Myotis lucifugus	ENSMLUG00000010942	1 retrocopy	retro_mluc_83,
Monodelphis domestica	ENSMODG00000014619	1 retrocopy	retro_mdom_347,
Mustela putorius furo	ENSMPUG00000015241	1 retrocopy	retro_mputfur_1435,
Mus musculus	ENSMUSG00000020492	2 retrocopies	retro_mmus_370, retro_mmus_778 ,
Otolemur garnettii	ENSOGAG00000026072	4 retrocopies	retro_ogar_1882, retro_ogar_2937, retro_ogar_3032, retro_ogar_907,
Rattus norvegicus	ENSRNOG00000025981	3 retrocopies	retro_rnor_1606, retro_rnor_523, retro_rnor_733,
Sorex araneus	ENSSARG00000011128	2 retrocopies	retro_sara_60, retro_sara_662,
Ictidomys tridecemlineatus	ENSSTOG00000024169	4 retrocopies	retro_itri_1115, retro_itri_1275, retro_itri_1434, retro_itri_725,
Tarsius syrichta	ENSTSYG00000006158	3 retrocopies	retro_tsyr_1620, retro_tsyr_2034, retro_tsyr_748,
Tursiops truncatus	ENSTTRG00000017196	1 retrocopy	retro_ttru_143,