RetrogeneDB ID: retro_ecab_355

Retrocopy location

• Organism: Horse (Equus caballus)
• Coordinates: 16:1308788..1309689(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PSMC1
• Ensembl ID: ENSECAG00000003601
• Aliases: None
• Description: proteasome (prosome, macropain) 26S subunit, ATPase, 1 [Source:HGNC Symbol;Acc:9547]

Sequence

>retro_ecab_355
TTATCAAAGTTAAGGAGAATTAAAGACTATCTTCTCATGGAGGAAGAATTCATTAGAAATCAGGAACAAATGAAGCCTTT
AGAAGAAAAGCAAGGGGAGGAAAGATGAAAGGTGGATGATCTAAGGGGGACCCCAATGTTGGTAGGAGCCTTAGAAGAGA
TCATTGATGACAATCACGCTGTCATGTCTACATCTGTGGGCTCAGGACACTACATCAGCATTCTTTCATTTGTAGCCAAG
GATCTGCTGGAACCAGGCTGCTTGGTCCTGTTCAGCCATAAGGTGCATGCCGTGATAGAGGTGCTGATGGGTGACACAGG
TCCCCTGGTCACAGTGATGAAGGTGGAAAAGGCCCCCAGGAGACCTGTGCTGATATTGGGGGCTTGGGCAACAAAACCCA
TGAAATTAGGAAATCTCTGGAGCTTCCTTTCACTCATCCTGAATATTATGAAGAGAGGGATATAAAGGCCCCTAAGGGGG
TCATTCTCTATGGTCCACCTGGCACATGTAAAACCTTACTAGCCAATGCAGTAGCAAACTAAACCTCAGCCACTTTCTTG
AGTGTGGTTGGTTCTGAATTTATTCAGAAGTACCTGGGTGATGAGCCCAAACTCGTACAGGAATTGTTTCAAGTTGCTGA
AGAACATGTACCATCCATCGTATTTATTGATAAAATTGATGCCATTGGGACAAAAAGATATGACTCAAATTCTGGTGGTG
AGAGAGAAATTCAGCAAATAATGTTGGAACTGTTGAACCAGTTGGATGGATTTGATTCAGGGGAGATGTGAAAGTTATCA
TGGCCGCAAACCACATAGAAAATTTGGATCCAGCACTTATCAGACCAGGCCACACTGACAGGGAGATCAAACTCCTCCTG
CCCAATGAAAGGACTAATAAG

Alignment

ORF - retro_ecab_355 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 81.85 %
• Parental protein coverage: 68.41 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  LLKLERIKDYLLMEEEFIRNQEQMKPLEEKQEEERSKVDDLRGTPMSVGTLEEIIDDNHAIVSTSVGSEH
          L.KL.RIKDYLLMEEEFIRNQEQMKPLEEKQ.EER.KVDDLRGTPM.VG.LEEIIDDNHA..STSVGS.H
Retrocopy LSKLRRIKDYLLMEEEFIRNQEQMKPLEEKQGEER*KVDDLRGTPMLVGALEEIIDDNHAVMSTSVGSGH

Parental  YVSILSFVDKDLLEPGCSVLLNHKVHAVIGVLMDDTDPLVTVMKVEKAP-QETYADIGGLDNQIQEIKES
          Y.SILSFV.KDLLEPGC.VL..HKVHAVI.VLM.DT.PLVTVMKVEKAP.QET.ADIGGL.N...EI..S
Retrocopy YISILSFVAKDLLEPGCLVLFSHKVHAVIEVLMGDTGPLVTVMKVEKAP<QETCADIGGLGNKTHEIRKS

Parental  VELPLTHPEYYEEMGIKPPKGVILYGPPGTGKTLLAKAVANQTSATFLRVVGSELIQKYLGDGPKLVREL
          .ELP.THPEYYEE..IK.PKGVILYGPPGT.KTLLA.AVAN.TSATFL.VVGSE.IQKYLGD.PKLV.EL
Retrocopy LELPFTHPEYYEERDIKAPKGVILYGPPGTCKTLLANAVAN*TSATFLSVVGSEFIQKYLGDEPKLVQEL

Parental  FRVAEEHAPSIVFIDEIDAIGTKRYDSNSGGEREIQRTMLELLNQLDGFDS-RGDVKVIMATNRIETLDP
          F.VAEEH.PSIVFID.IDAIGTKRYDSNSGGEREIQ..MLELLNQLDGFDS.RGDVKVIMA.N.IE.LDP
Retrocopy FQVAEEHVPSIVFIDKIDAIGTKRYDSNSGGEREIQQIMLELLNQLDGFDS<RGDVKVIMAANHIENLDP

Parental  ALIRPGRIDRKIEFPLPDEKTKK
          ALIRPG..DR.I...LP.E.T.K
Retrocopy ALIRPGHTDREIKLLLPNERTNK

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	42.91 RPM
SRP021940_cerebellum	0.00 RPM	88.18 RPM
SRP021940_embryo	0.13 RPM	92.93 RPM
SRP021940_placental_villous	0.05 RPM	93.58 RPM
SRP021940_synovial_membrane	0.03 RPM	52.35 RPM
SRP021940_testis	0.00 RPM	191.96 RPM

ChIP-Seq

Equus caballus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ecab_355 retrocopy.

TSS

Equus caballus was not studied using FANTOM5 data.

Lab

retro_ecab_355 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ecab_355 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 17 parental genes, and 48 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000001839	4 retrocopies	retro_amel_1536, retro_amel_1886, retro_amel_405, retro_amel_962,
Canis familiaris	ENSCAFG00000017510	2 retrocopies	retro_cfam_1238, retro_cfam_1562,
Choloepus hoffmanni	ENSCHOG00000013595	1 retrocopy	retro_chof_1954,
Dasypus novemcinctus	ENSDNOG00000006458	1 retrocopy	retro_dnov_2162,
Equus caballus	ENSECAG00000003601	1 retrocopy	retro_ecab_355 ,
Echinops telfairi	ENSETEG00000002661	1 retrocopy	retro_etel_580,
Felis catus	ENSFCAG00000011310	8 retrocopies	retro_fcat_1444, retro_fcat_1559, retro_fcat_2015, retro_fcat_344, retro_fcat_614, retro_fcat_691, retro_fcat_713, retro_fcat_924,
Macropus eugenii	ENSMEUG00000001526	1 retrocopy	retro_meug_623,
Myotis lucifugus	ENSMLUG00000007471	2 retrocopies	retro_mluc_2490, retro_mluc_508,
Macaca mulatta	ENSMMUG00000022990	1 retrocopy	retro_mmul_255,
Mustela putorius furo	ENSMPUG00000008150	4 retrocopies	retro_mputfur_1602, retro_mputfur_409, retro_mputfur_654, retro_mputfur_815,
Mus musculus	ENSMUSG00000021178	3 retrocopies	retro_mmus_1517, retro_mmus_1826, retro_mmus_812,
Oryctolagus cuniculus	ENSOCUG00000006231	4 retrocopies	retro_ocun_1135, retro_ocun_1212, retro_ocun_1654, retro_ocun_411,
Otolemur garnettii	ENSOGAG00000032343	2 retrocopies	retro_ogar_3014, retro_ogar_367,
Pongo abelii	ENSPPYG00000025948	9 retrocopies	retro_pabe_1059, retro_pabe_153, retro_pabe_2379, retro_pabe_2408, retro_pabe_2737, retro_pabe_2832, retro_pabe_3099, retro_pabe_825, retro_pabe_907,
Pteropus vampyrus	ENSPVAG00000010020	3 retrocopies	retro_pvam_1190, retro_pvam_350, retro_pvam_500,
Tursiops truncatus	ENSTTRG00000013582	1 retrocopy	retro_ttru_239,