RetrogeneDB ID: retro_mmus_3559

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: X:166485601..166486351(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMUSG00000081875
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Tcea1
• Ensembl ID: ENSMUSG00000033813
• Aliases: Tcea1, S-II
• Description: transcription elongation factor A (SII) 1 [Source:MGI Symbol;Acc:MGI:1196624]

Sequence

>retro_mmus_3559
GCTGCCACACTGGATTTGCTGAAAGAGCTTAAGAATATTCCTATGACCCTGGAATTGCTATAATCCACGAGAATTGGAAT
GTCTGTCATTGCTCTTCGCAAGCAGAGTACAGATGAAGAAGTCACATTTCTAGCCAAATCTCTCATCAAATCCTGGAGAA
AATTATTAGATGGACCGTCAACTGATAAAGACCCAGAAGAAAGAAAAAAGAACCTACAATTTCATCACAGAATAGCCCTG
AAGCTAGAGAAGAAAGTAGTTCCAGCAGCAATGTAAGCAGCAGAAAGGATGAGACAAATGCTCGAGATACTTATGTTTCA
TCTTTTCCTCGGGCACCAAGCACTTCTGATTCTGTGTGATTAAAGTGTAGGGAGATGCTTGCTACAGCTCTCCAGACAAG
AGATAATTATGTTGCTATTGGAGCTGATGAAGAAGAAGTGGGATCTCAGATTGAGGAAGCTATATATCAAGGAATAAGGA
ATACAGACATGAAATACAAAAACGGAGTATGAAGTAGGATATCAAATCTTAAAGATGCAAAGAATCCAAATTTAAGGAAA
AATGTGCTGTGTGGGAATGTTCCTCCTAACCTATTTGCTAGAATGACAGCAGAGGAAATGGCTAGTAATGAGCTCAAAGA
GATGAGGAAAAACCTGACCAAAGAAGCCATCAAGGAAGCATCAGATGGCCAAGACTGCTGGGACCCAGACTGACTTGTTC
ACTTGTGGCAAATGTAAAAAGAACTGCACT

Alignment

ORF - retro_mmus_3559 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 90.51 %
• Parental protein coverage: 83.39 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  AGALDLLKELKNIPMTLELLQSTRIGMSVNALRKQSTDEEVTSLAKSLIKSWKKLLDGPSTDKDPEE-KK
          A..LDLLKELKNIPMTLELL.STRIGMSV.ALRKQSTDEEVT.LAKSLIKSW.KLLDGPSTDKDPEE.KK
Retrocopy AATLDLLKELKNIPMTLELL*STRIGMSVIALRKQSTDEEVTFLAKSLIKSWRKLLDGPSTDKDPEE<KK

Parental  KEPAISSQNSPEAREESSSSSNVSSRKDETNARDTYVSSFPRAPSTSDSVRLKCREMLAAALRTGDDYVA
          KEP.ISSQNSPEAREESSSSSNVSSRKDETNARDTYVSSFPRAPSTSDSV.LKCREMLA.AL.T.D.YVA
Retrocopy KEPTISSQNSPEAREESSSSSNVSSRKDETNARDTYVSSFPRAPSTSDSV*LKCREMLATALQTRDNYVA

Parental  IGADEEELGSQIEEAIYQEIRNTDMKYKNRVRSRISNLKDAKNPNLRKNVLCGNIPPDLFARMTAEEMAS
          IGADEEE.GSQIEEAIYQ.IRNTDMKYKN.V.SRISNLKDAKNPNLRKNVLCGN.PP.LFARMTAEEMAS
Retrocopy IGADEEEVGSQIEEAIYQGIRNTDMKYKNGV*SRISNLKDAKNPNLRKNVLCGNVPPNLFARMTAEEMAS

Parental  DELKEMRKNLTKEAIRE-HQMAKTGGTQTDLFTCGKCKKKNCT
          .ELKEMRKNLTKEAI.E.HQMAKT.GTQTDLFTCGKC.KKNCT
Retrocopy NELKEMRKNLTKEAIKE>HQMAKTAGTQTDLFTCGKC-KKNCT

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	10.42 RPM
SRP007412_cerebellum	0.00 RPM	7.21 RPM
SRP007412_heart	0.00 RPM	4.17 RPM
SRP007412_kidney	0.00 RPM	9.03 RPM
SRP007412_liver	0.00 RPM	7.67 RPM
SRP007412_testis	0.00 RPM	8.78 RPM

ChIP-Seq

RNA Polymerase II activity near the 5' end of retro_mmus_3559 was not detected

EST

No EST(s) were mapped for retro_mmus_3559 retrocopy.

TSS

No TSS is located nearby retro_mmus_3559 retrocopy 5' end.

Lab

retro_mmus_3559 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_3559 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 16 parental genes, and 32 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000001247	1 retrocopy	retro_chof_458,
Callithrix jacchus	ENSCJAG00000014407	1 retrocopy	retro_cjac_2095,
Dasypus novemcinctus	ENSDNOG00000013799	4 retrocopies	retro_dnov_1315, retro_dnov_1853, retro_dnov_839, retro_dnov_952,
Erinaceus europaeus	ENSEEUG00000009220	1 retrocopy	retro_eeur_73,
Homo sapiens	ENSG00000187735	4 retrocopies	retro_hsap_2634, retro_hsap_4159, retro_hsap_4200, retro_hsap_4243,
Gorilla gorilla	ENSGGOG00000023652	3 retrocopies	retro_ggor_2794, retro_ggor_2814, retro_ggor_2844,
Macaca mulatta	ENSMMUG00000016022	1 retrocopy	retro_mmul_1146,
Mus musculus	ENSMUSG00000033813	2 retrocopies	retro_mmus_1369, retro_mmus_3559 ,
Nomascus leucogenys	ENSNLEG00000000981	3 retrocopies	retro_nleu_1028, retro_nleu_1374, retro_nleu_1384,
Oryctolagus cuniculus	ENSOCUG00000007474	3 retrocopies	retro_ocun_1382, retro_ocun_401, retro_ocun_852,
Pongo abelii	ENSPPYG00000018589	3 retrocopies	retro_pabe_3395, retro_pabe_3436, retro_pabe_3455,
Pan troglodytes	ENSPTRG00000020251	2 retrocopies	retro_ptro_2851, retro_ptro_2884,
Rattus norvegicus	ENSRNOG00000022323	1 retrocopy	retro_rnor_1089,
Sarcophilus harrisii	ENSSHAG00000013661	1 retrocopy	retro_shar_50,
Ictidomys tridecemlineatus	ENSSTOG00000021179	1 retrocopy	retro_itri_1745,
Tarsius syrichta	ENSTSYG00000001030	1 retrocopy	retro_tsyr_1624,