RetrogeneDB ID: retro_ecab_432

Retrocopy location

• Organism: Horse (Equus caballus)
• Coordinates: 18:43357750..43358321(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: COQ2
• Ensembl ID: ENSECAG00000012542
• Aliases: None
• Description: coenzyme Q2 4-hydroxybenzoate polyprenyltransferase [Source:HGNC Symbol;Acc:25223]

Sequence

>retro_ecab_432
AATACAGCTCTGAGAGAAGGATCCCTACTTCTTGTCATCACCTACCCACTAACAGAAAGAATTACATACTGGCGCCAATT
AGTCTTAGCTTTGGGGTTGACTTTTAATTGAAGAGTGTTCCTTGGATGGTCTGTTATCAAGGGTCCCTATGATCCATCTG
TTCACCTGCCTCTTCCTTTTTCTGGAATTGCATGTGCACTAATATATGATACTATTATGCCTATCAGGACAAAAGAGATG
ATGTTCCGATTGGTCTTAAGTCCACAACACTGCAGCTCAGTGAAAACACCAAGCAGTGGCTCAGTGGCTTCAGCATCGTG
ATGCTGGAGGGACTGAGCCTGTGGGAGTGAACAGTGATCAGACCCCTCCCTACAGCCCTGCTCTGGCTGCTGGAGACCAA
GTGGCTTGTCAGATCTACACTCTAGACATCCGCTCTTGAGGATTGTGGAAATAAATTTACCTCCAACCAAACAATATGAC
TAATGGTCTTCTAGAGATTGTCCTTGGGAATTTGTGGAAAGAAAAGAAGACAGACCAAATGAAGAAAAATATAGACAGCA
GAATAGAAAAT

Alignment

ORF - retro_ecab_432 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 63.96 %
• Parental protein coverage: 66.32 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  SVALGAASLLLVITYPLMKRVTYWPQL--ALGLAFNWGALLGWSAVKGSCDPSVCLPLYFSGIMWTLIYD
          ..AL...SLLLVITYPL..R.TYW.QL..ALGL.FN....LGWS..KG..DPSV.LPL.FSGI...LIYD
Retrocopy NTALREGSLLLVITYPLTERITYWRQLVLALGLTFN*RVFLGWSVIKGPYDPSVHLPLPFSGIACALIYD

Parental  TI-YAHQDKKDDALIGLKSTALWFREDTKQWLSGFSVAMVGALSL-VGVSSEQTAPYYAALAAVGAHLAR
          TI.YA.QDK.DD..IGLKST.L...E.TKQWLSGFS..M...LSL.VGV.S.QT.PY..ALAA.G...A.
Retrocopy TI<YAYQDKRDDVPIGLKSTTLQLSENTKQWLSGFSIVMLEGLSL<VGVNSDQTPPYSPALAA-GDQVAC

Parental  QIYTLDIHRPEDCW-DKFTSNRTVGLIIF-LGIVLGNLWKQKKTDETKKKIDYVIEN
          QIYTLDI.R....W..KFTSN.T..L..F.L.IVLGNLWK.KKTD..KK.ID..IEN
Retrocopy QIYTLDI-RS*GLW>NKFTSNQTI*LMVF<LEIVLGNLWKEKKTDQMKKNIDSRIEN

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	4.31 RPM
SRP021940_cerebellum	0.00 RPM	9.40 RPM
SRP021940_embryo	0.00 RPM	9.16 RPM
SRP021940_placental_villous	0.00 RPM	15.97 RPM
SRP021940_synovial_membrane	0.00 RPM	5.22 RPM
SRP021940_testis	0.00 RPM	6.14 RPM

ChIP-Seq

Equus caballus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ecab_432 retrocopy.

TSS

Equus caballus was not studied using FANTOM5 data.

Lab

retro_ecab_432 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ecab_432 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 8 parental genes, and 37 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000005006	1 retrocopy	retro_amel_1898,
Bos taurus	ENSBTAG00000005744	1 retrocopy	retro_btau_1835,
Cavia porcellus	ENSCPOG00000011458	1 retrocopy	retro_cpor_1202,
Equus caballus	ENSECAG00000012542	1 retrocopy	retro_ecab_432 ,
Myotis lucifugus	ENSMLUG00000015267	1 retrocopy	retro_mluc_1776,
Mus musculus	ENSMUSG00000029319	1 retrocopy	retro_mmus_2883,
Tarsius syrichta	ENSTSYG00000013801	30 retrocopies	retro_tsyr_1015, retro_tsyr_1155, retro_tsyr_1173, retro_tsyr_1180, retro_tsyr_1207, retro_tsyr_1235, retro_tsyr_1327, retro_tsyr_1335, retro_tsyr_1385, retro_tsyr_1451, retro_tsyr_1491, retro_tsyr_1646, retro_tsyr_1709, retro_tsyr_1742, retro_tsyr_2015, retro_tsyr_2062, retro_tsyr_2087, retro_tsyr_2136, retro_tsyr_2146, retro_tsyr_466, retro_tsyr_513, retro_tsyr_533, retro_tsyr_54, retro_tsyr_548, retro_tsyr_607, retro_tsyr_619, retro_tsyr_654, retro_tsyr_776, retro_tsyr_839, retro_tsyr_995,
Tursiops truncatus	ENSTTRG00000005647	1 retrocopy	retro_ttru_1726,