RetrogeneDB ID: retro_btau_269

Retrocopy location

• Organism: Cow (Bos taurus)
• Coordinates: 1:93601621..93601962(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: ANAPC15
• Ensembl ID: ENSBTAG00000002999
• Aliases: ANAPC15, APC15, C15H11orf51
• Description: Anaphase-promoting complex subunit 15 [Source:UniProtKB/Swiss-Prot;Acc:Q3SZ31]

Sequence

>retro_btau_269
ATGTCCACCTTGCTGTCGTCACTCTTGTCTCATGTGACTGAGACACTGTGGTTGAATCTGGATGGATCCTGGATGGAGGA
GACAGGCACAGCTGCAGGACAGCAGCATGAAGCCTGGCTCCAAAGCATCACACGGAAAAACAGAAACTTGGTATTTCTTT
GGCAAGCTAGACTCAGACCACTATGACAAGAAGGAGAAGGAGGATTAAGATGGCCAGGAGAGAGGACACTCAGAGGACAG
TGAGGACATGGGTGAGATGAATGATTACAATGAGTAGCCTGATGATGGAGAATCATTGAGACGGACACGAAAGCAACAGA
AAGAATTAGGGCCAGTGGATG

Alignment

ORF - retro_btau_269 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 53.66 %
• Parental protein coverage: 99.17 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  MSTLFPSLFPRVTETLWFNLDRPCVEETELQQQEQQHQAWLQSIAEKDNNLVPI-GKPASEHYDDEEEED
          MSTL..SL...VTETLW.NLD....EET......QQH.AWLQSI..K..NLV...GK..S.HYD....E.
Retrocopy MSTLLSSLLSHVTETLWLNLDGSWMEETGTAAG-QQHEAWLQSITRKNRNLVFL>GKLDSDHYD--KKEK

Parental  EDDDEDSEEDSEDDEDMQDMDEMNDYNESPDDGE-VNEVDM-EGNEQDQDQWM
          ED.D......SED.E...DM.EMNDYNE.PDDGE...E.D..E.N.....QWM
Retrocopy ED*DGQERGHSEDSE---DMGEMNDYNE*PDDGE<IIETDT<ESNRKN*GQWM

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
ERP005899_liver	0.00 RPM	8.36 RPM
ERP005899_muscle	0.00 RPM	19.37 RPM
SRP017611_brain	0.00 RPM	16.81 RPM
SRP017611_kidney	0.00 RPM	14.82 RPM
SRP017611_liver	0.00 RPM	9.36 RPM
SRP030211_testis	0.00 RPM	35.66 RPM

ChIP-Seq

Bos taurus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_btau_269 retrocopy.

TSS

Bos taurus was not studied using FANTOM5 data.

Lab

retro_btau_269 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_btau_269 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Gorilla gorilla	retro_ggor_1999
Pongo abelii	retro_pabe_2388
Equus caballus	retro_ecab_470

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Parental genes homology:

Parental genes homology involve 16 parental genes, and 20 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000010843	1 retrocopy	retro_amel_298,
Bos taurus	ENSBTAG00000002999	2 retrocopies	retro_btau_252, retro_btau_269 ,
Canis familiaris	ENSCAFG00000005781	1 retrocopy	retro_cfam_1752,
Equus caballus	ENSECAG00000021041	1 retrocopy	retro_ecab_470,
Felis catus	ENSFCAG00000005321	1 retrocopy	retro_fcat_1350,
Homo sapiens	ENSG00000110200	1 retrocopy	retro_hsap_4780,
Gorilla gorilla	ENSGGOG00000012501	2 retrocopies	retro_ggor_1999, retro_ggor_2977,
Myotis lucifugus	ENSMLUG00000014120	1 retrocopy	retro_mluc_238,
Macaca mulatta	ENSMMUG00000016270	1 retrocopy	retro_mmul_2551,
Mustela putorius furo	ENSMPUG00000010260	1 retrocopy	retro_mputfur_596,
Nomascus leucogenys	ENSNLEG00000017234	1 retrocopy	retro_nleu_1100,
Pongo abelii	ENSPPYG00000003646	2 retrocopies	retro_pabe_2388, retro_pabe_3720,
Pteropus vampyrus	ENSPVAG00000015797	1 retrocopy	retro_pvam_404,
Sorex araneus	ENSSARG00000004171	2 retrocopies	retro_sara_444, retro_sara_686,
Tarsius syrichta	ENSTSYG00000014179	1 retrocopy	retro_tsyr_35,
Tursiops truncatus	ENSTTRG00000010773	1 retrocopy	retro_ttru_277,