RetrogeneDB ID: retro_ecab_941

Retrocopy location

• Organism: Horse (Equus caballus)
• Coordinates: 7:88922965..88924126(+)
• Located in intron of: ENSECAG00000024835

Retrocopy information

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

Parental gene information

• Parental gene symbol: IDH3G
• Ensembl ID: ENSECAG00000018509
• Aliases: None
• Description: isocitrate dehydrogenase 3 (NAD+) gamma [Source:HGNC Symbol;Acc:5386]

Sequence

>retro_ecab_941
GTGGCCCTGAAGATGCTGACAGCTGCCGGTTTCTCTGGGAAGGCCATGTTCCGACCTTCCATTCTTGGCCATTCTTGGGA
GATCTTACTTGGCCGTGAAACCTCCCTGAGGAGCTTTTCTTCTAAACACAATATTCCTCCATCAGCCAAGTATGGTGGGC
GGCACACTGTGACTATGATTCCTGGGGATGGCATCGGGCCTGAACTTATGCTGCATGTCAAGACTGTGTTCAGACGTATG
TGTGTGCCTGTGGACTTTGAGGAGGTGCAGGTTAACTCCACTTCTTGCGAAGAGGACGTGCATAATGCCATCATGGCAGT
CCGTCGAAACCGTGTGGCCTTGAAGGGCAACATTGAAACTGACCACAGTCTGCCACCATCTCACAAATCCCGCAACAGCC
TGTTTCGCACCATGCTAGATCTCTATGCCAGTGTCATCCATTTTCAGAGTCTGCCGGGTGTGGAGACCCGGCACAAGAAC
GTAGACATCTTAGTTGTTCGGGAAAACACAGAGGGTGAATACAGCAACCTGGAGCATGAGAGTGTGAAAGGAGTGATAGA
GAGCCTAAAGATCATCACTAAGGCCAAGTCTTTGCGCATTGCTGAATATGCCTTCCAGCTGGCCCAGGACATGGGGCGCA
AGAAAGTGACAGCTGTGCACAAGGCCAACATCATGAAATTGGGAGATGGTCTCTTCCTCCAGTGCTGTAGGGAGGTGGCC
TCCCACTATCCTCAGCTCACCTTTGAAAGCATGATTGTCGATAACACTACCATGCAGCTGGTATCCCGCCCCCAGCAGTT
TGATGTCATGGTGATGCCCAATCTTTATGGCAACATTGTCAACAATGTCTGCACAGGGTTGGTTGGAGGAGCAGGGCTTG
TGCCTGGTGCCAACTATGGACACATATATGCAGTGTTTGAAACAGCTTCAAAGCAATCTGGCAAGAATATAGCCAATAAG
AATATGGCTAACCCTACTGCCATGCTGCTGTCGAGTTGTATTATGCTGGATTACCTCAAGCTTCACTCCTATGCCACTTC
CATACGTACTGCAGTCTTGGCATCCGTGGAGAATAAAAGTGTCCATACTCCAGACATTGGAGGCCAGAGTACCACATTGG
ATTTCATTCAAAATATCATCAACCACATCGATACTGTCAAT

Alignment

ORF - retro_ecab_941 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 76.74 %
• Parental protein coverage: 98.47 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MALKVATAAGGAAKAVLRPTLLCRPWEVLGAPRAPRRSFSQR-TIPPSAKYGGRHTVTMIPGDGIGPELM
          .ALK..TAAG...KA..RP..L...WE.L.......RSFS....IPPSAKYGGRHTVTMIPGDGIGPELM
Retrocopy VALKMLTAAGFSGKAMFRPSILGHSWEILLGRETSLRSFSSKHNIPPSAKYGGRHTVTMIPGDGIGPELM

Parental  LHVKSVFRHACVPVDFEEVHVSSSADEEDIRNAIMAIRRNRVALKGNIETNHNLPPSHKSRNNILRTSLD
          LHVK.VFR..CVPVDFEEV.V.S...EED..NAIMA.RRNRVALKGNIET.H.LPPSHKSRN...RT.LD
Retrocopy LHVKTVFRRMCVPVDFEEVQVNSTSCEEDVHNAIMAVRRNRVALKGNIETDHSLPPSHKSRNSLFRTMLD

Parental  LYANVIHCKSLPGVVTRHRDIDILIVRENTEGEYSSLEHESVAGVVESLKIITKAKSLRIAEYAFKLAQE
          LYA.VIH..SLPGV.TRH...DIL.VRENTEGEYS.LEHESV.GV.ESLKIITKAKSLRIAEYAF.LAQ.
Retrocopy LYASVIHFQSLPGVETRHKNVDILVVRENTEGEYSNLEHESVKGVIESLKIITKAKSLRIAEYAFQLAQD

Parental  CGRKKVTAVHKANIMKLGDGLFLQCCKEVAAGYPQITFENMIVDNTTMQLVSRPQQFDVMVMPNLYGNIV
          .GRKKVTAVHKANIMKLGDGLFLQCC.EVA..YPQ.TFE.MIVDNTTMQLVSRPQQFDVMVMPNLYGNIV
Retrocopy MGRKKVTAVHKANIMKLGDGLFLQCCREVASHYPQLTFESMIVDNTTMQLVSRPQQFDVMVMPNLYGNIV

Parental  NNVCAGLVGGPGLVAGANYGHVYAVFETATRNTGKSIANKNVANPTATLLASCMMLDHLKLHSYATSIRK
          NNVC.GLVGG.GLV.GANYGH.YAVFETA....GK.IANKN.ANPTA.LL.SC.MLD.LKLHSYATSIR.
Retrocopy NNVCTGLVGGAGLVPGANYGHIYAVFETASKQSGKNIANKNMANPTAMLLSSCIMLDYLKLHSYATSIRT

Parental  AVLASMDNENMHTPDIGGQGTTSEAIQDIIRHIRIIN
          AVLAS..N...HTPDIGGQ.TT...IQ.II.HI...N
Retrocopy AVLASVENKSVHTPDIGGQSTTLDFIQNIINHIDTVN

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	33.71 RPM
SRP021940_cerebellum	0.00 RPM	102.05 RPM
SRP021940_embryo	0.08 RPM	67.26 RPM
SRP021940_placental_villous	0.24 RPM	25.16 RPM
SRP021940_synovial_membrane	0.03 RPM	40.16 RPM
SRP021940_testis	169.77 RPM	28.01 RPM

ChIP-Seq

Equus caballus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ecab_941 retrocopy.

TSS

Equus caballus was not studied using FANTOM5 data.

Lab

retro_ecab_941 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ecab_941 has 7 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_759
Pan troglodytes	retro_ptro_534
Mus musculus	retro_mmus_134
Oryctolagus cuniculus	retro_ocun_80
Bos taurus	retro_btau_1194
Sus scrofa	retro_sscr_662
Canis familiaris	retro_cfam_1023

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Parental genes homology:

Parental genes homology involve 18 parental genes, and 18 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000018466	1 retrocopy	retro_amel_1892,
Bos taurus	ENSBTAG00000001059	1 retrocopy	retro_btau_1194,
Canis familiaris	ENSCAFG00000019286	1 retrocopy	retro_cfam_1023,
Callithrix jacchus	ENSCJAG00000011185	1 retrocopy	retro_cjac_1597,
Equus caballus	ENSECAG00000018509	1 retrocopy	retro_ecab_941 ,
Homo sapiens	ENSG00000067829	1 retrocopy	retro_hsap_759,
Latimeria chalumnae	ENSLACG00000007365	1 retrocopy	retro_lcha_17,
Loxodonta africana	ENSLAFG00000006904	1 retrocopy	retro_lafr_560,
Macropus eugenii	ENSMEUG00000013934	1 retrocopy	retro_meug_203,
Myotis lucifugus	ENSMLUG00000004457	1 retrocopy	retro_mluc_396,
Mustela putorius furo	ENSMPUG00000008781	1 retrocopy	retro_mputfur_644,
Mus musculus	ENSMUSG00000002010	1 retrocopy	retro_mmus_134,
Nomascus leucogenys	ENSNLEG00000013540	1 retrocopy	retro_nleu_394,
Otolemur garnettii	ENSOGAG00000006735	1 retrocopy	retro_ogar_25,
Pteropus vampyrus	ENSPVAG00000013163	1 retrocopy	retro_pvam_373,
Rattus norvegicus	ENSRNOG00000037284	1 retrocopy	retro_rnor_209,
Sus scrofa	ENSSSCG00000012783	1 retrocopy	retro_sscr_662,
Tursiops truncatus	ENSTTRG00000011728	1 retrocopy	retro_ttru_848,