RetrogeneDB ID: retro_ecab_1074

Retrocopy location

• Organism: Horse (Equus caballus)
• Coordinates: X:56927347..56928043(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSECAG00000012456
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: TRAPPC13
• Ensembl ID: ENSECAG00000011983
• Aliases: None
• Description: trafficking protein particle complex 13 [Source:HGNC Symbol;Acc:25828]

Sequence

>retro_ecab_1074
AGTTCAGAGATGAGTGATTTATTTCTTGAAGTCCAGATTCAGAATATTTCATCTTCAACTGTCTTTATACAAAAGGTTTC
CTTAAAGCCATCTGAAATGTACACTGGGGCAGAATTAAATACCGTTAATCAGGCTGGAGAAGATGAGTGCACCTTTGGAA
CGAGACCAATTTTGCAGTCAATGGAAGGACGCCAGTATTTATACCACCTTCAGCTCAAGCAGGAATTTTCAGAGAAAGCT
GGTACCATTAGGGGACTAACAGAAATGGGAAAATTGGACATAGAGTGGAAAAGAAATCCAGGTGAAATGGCAATACTACG
GACAATCCAACTTGAAAGAGAGGCCCTAGTTTATGGAAACATGAAGCTATCTTTGGAGACAATCCCAGATACTGTAATTC
TAGAAGAGCCTTTTCATATTACCTGTAAGATAACAAACTGTGGTGATAGGAAAATGAAATTGTTTTTGAAGACGTGTGAT
ACAGATTCTATTCGTTGGTGTGGAAGTTCAGGAAGGTATCTTGGAAAGCTGCCACCAAATTCATCTCTCCACTTTACTCT
GACACTACTGTCCTTAAAACTGGGCCTGCAAAGTGTCTCTGGCATATGGATAACAGAAAAGTTATTAAAGAAAACATATG
TCTGTGATGATGTTGCAAAAGTCTGTGTAATATCTTCCATGATTAAAATGAAAAGC

Alignment

ORF - retro_ecab_1074 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 61.21 %
• Parental protein coverage: 57.71 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  NSVTDEVFLEAQIQNITTSPMFMEKVSLEPSIMYNVAELNSVNQAGECVTTFGSRAYLQPMDTRQYLYCL
          .S.....FLE.QIQNI..S..F..KVSL.PS.MY..AELN.VNQAGE...TFG.R..LQ.M..RQYLY.L
Retrocopy SSEMSDLFLEVQIQNISSSTVFIQKVSLKPSEMYTGAELNTVNQAGEDECTFGTRPILQSMEGRQYLYHL

Parental  KPKKEFAEKAGIIKGVTVIGKLDIVWKTNLGERGRLQTSQLQRMAPGYGDVRLSLEAIPDTVNLEEPFHI
          ..K.EF.EKAG.I.G.T..GKLDI.WK.N.GE...L.T.QL.R.A..YG...LSLE.IPDTV.LEEPFHI
Retrocopy QLKQEFSEKAGTIRGLTEMGKLDIEWKRNPGEMAILRTIQLEREALVYGNMKLSLETIPDTVILEEPFHI

Parental  TCKITNCSERTMDLVLEMCNTSSIHWCGISGRQLGKLHPSSSLCLALTLLSSVQGLQSVSGLRLTDTFLK
          TCKITNC..R.M.L.L..C.T.SI.WCG.SGR.LGKL.P.SSL...LTLLS...GLQSVSG...T...LK
Retrocopy TCKITNCGDRKMKLFLKTCDTDSIRWCGSSGRYLGKLPPNSSLHFTLTLLSLKLGLQSVSGIWITEKLLK

Parental  RTYEYDDIAQVCVVSSAVKVES
          .TY..DD.A.VCV.SS..K..S
Retrocopy KTYVCDDVAKVCVISSMIKMKS

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
SRP021940_articular_cartilage	0.00 RPM	3.01 RPM
SRP021940_cerebellum	0.05 RPM	5.87 RPM
SRP021940_embryo	0.00 RPM	5.04 RPM
SRP021940_placental_villous	0.00 RPM	6.88 RPM
SRP021940_synovial_membrane	0.00 RPM	4.58 RPM
SRP021940_testis	0.90 RPM	2.17 RPM

ChIP-Seq

Equus caballus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ecab_1074 retrocopy.

TSS

Equus caballus was not studied using FANTOM5 data.

Lab

retro_ecab_1074 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ecab_1074 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 8 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000006026	1 retrocopy	retro_chof_1834,
Dasypus novemcinctus	ENSDNOG00000006386	1 retrocopy	retro_dnov_1288,
Equus caballus	ENSECAG00000011983	1 retrocopy	retro_ecab_1074 ,
Pteropus vampyrus	ENSPVAG00000008275	1 retrocopy	retro_pvam_980,
Sorex araneus	ENSSARG00000000639	1 retrocopy	retro_sara_394,
Ictidomys tridecemlineatus	ENSSTOG00000021318	1 retrocopy	retro_itri_1455,
Tarsius syrichta	ENSTSYG00000004582	1 retrocopy	retro_tsyr_18,
Tursiops truncatus	ENSTTRG00000006537	1 retrocopy	retro_ttru_1068,