RetrogeneDB ID: retro_ecab_7

Retrocopy location

• Organism: Horse (Equus caballus)
• Coordinates: X:17345722..17347597(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSECAG00000006351
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: DDX43
• Ensembl ID: ENSECAG00000017971
• Aliases: None
• Description: DEAD (Asp-Glu-Ala-Asp) box polypeptide 43 [Source:HGNC Symbol;Acc:18677]

Sequence

>retro_ecab_7
ATGGCCTGGGCCCCCGAGTGGAGGAGGGCAGAGCCTCGAGATGGCAGGGCCAGCCGGGATGGCAGGGGCGGCACGGGCGG
CAGCGGCCTCTCCAGGTACTGGGAGCCGAGGGCCTTTGGCTCCCGGGAACCACCCCTGTGCTTCAGAATAAAGAACAGTA
TGGTTGGCGTGGTGATTGGTCGCGGAGGGTCAAAGATAAAAGACATCCAGAGTATGACGAGCACCAAAATACAGATCGTA
AAAGGTGACTCTGAAGCCGAGGTCAAGATTTTTGGCAGCGAAGCCATGAAGGGAAAAGCGAAAGCACTTATACAAACCCT
CGTGCGAAAACAAGAAGGAAGGTACAGTTCGGTAGCCAGTGTAGATAATGCCGCCTCCCAGTCCTCTGCTGGGAGAGACT
TACGCACACGCCCCGTTGTTAGACAAGTGCGGCCGCTGATAGACTGGGATCACGTTAAGGCAGAAGGGGCGGCATGGGCA
AAAAGAAAATGGGCGGATTTACCACCAATCAAGAAAAACTTCTACGTAGAATCCACAGCAACAAGCTCGCTGTCTCAAGT
GCAAGTAGACGCTTGGAGACAGGAAAATTTCAACATAACGTGTGAGGACCTGAAAGACGGCGAAAAACGTCCCATCCCCA
ACCCGACCTGTAAATTTGAGGATGCCTTTGAGCACTATCCCGAGGTCCTGAAAAGCATTAAGAAAGCAGGTTTCCAAAGG
CCAACGCCCATTCAGTCACAGGCATGGCCGATTGTGCTACAAGGAATGGATCTGATAGGAGTTGCCCAAACCGGGACAGG
CAAGACCTTGTCTTATTTGATACCCGGCTTTATTCACCTTGATTCGCAGCCCATATCTAGAGAAGAAAGAAATGGGCCTG
GCATGCTCGTCCTCACCCCCACGCGAGAGCTAGCTCTTCAGGTCGAGGCAGAATGTTCTAAGTATTCCTACAAAGGTCTT
AAAAGCGTTTGTGTATACGGCGGTGGAAACAGAAAAGAGCAAATTCAGCACATTACCAAAGGCGTCGACATCATTATTGC
AACTCCTGGACGACTGAATGATCTGCAGATGAACAAGTGTGTCAACCTACGAAGCATCACTTACTTGGTGTTAGACGAAG
CGGATAAAATGTTGGATCTGGGCTTTGAAGGCCAGATCACGAAGATTCTACTAGATGTGCGCCCAGACCGGCAGACTGTT
ATGACAAGTGCAACGTGGCCACACACCATTCGCCAACTTGCAAGATCTTATTTGAAAGAGCCTATGATTGTTTATGTCGG
TACTCTAGATCTCGTTGCTGTCCATACAGTGAAGCAAGACATCATTGTCACCACAGAGGAAGAAAAACGAACTCTTATCC
AAGAATTCCTACGGAACCTGGCACCCGAAGACAAAGCTATCATATTTGTCAGCAGAAAGCTGGTTGCAGATGACTTATCA
AGCGATCTGAGCATCCAGGGCGTCCCGGTACAATCCCTGCACGGCAACAGAGAGCAGTTTGACCGCGAGCAGGCGTTAGA
CGACTTCCGAAGTGGAAGAGTGAAGATATTGATTGCTACCGATTTAGCAGCCCGAGGCCTCGATGTCAGGGATGTCACAC
ACGTATACAACTACGATTCCCCAAAGAATCTTGAAGAATACGTGCATAGAGTAGGGCGTACTGGAAGAGCAGGCAAGACT
GGAGTCTCTGTCACCCTTATGACTCAAGCTGACTGGAAGATTGCCACTGAATTGATTAAAATTCTGGAAAGAGCTAATCA
AAGTGTCCCAGAAGATCTTCTGAAAATGGCAGAGCAATGCAAGTTGCAGAAAGGAAAAAAGGACTCAGGCAATGGAGCCA
GAAACCCTCAAGGAAAAGCCAAGCAGTTTTACTGA

Alignment

ORF - retro_ecab_7 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 74.2 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  GHGGSKIRDIQSTTNTKIQIIKGYPEAEVKIFGSKMMQTKAKAVIDNLVKKQE-NYNSEPRVDIVALHPS
          G.GGSKI.DIQS.T.TKIQI.KG..EAEVKIFGS..M..KAKA.I..LV.KQE..Y.S...VD..A...S
Retrocopy GRGGSKIKDIQSMTSTKIQIVKGDSEAEVKIFGSEAMKGKAKALIQTLVRKQEGRYSSVASVDNAASQSS

Parental  AGRGVRANVSVVTEDQPLIDWDQIREEGLKWEKKKWADLPLIKKNFYMESETTSSMSQMQVDNWRKENYN
          AGR..R....VV....PLIDWD....EG..W.K.KWADLP.IKKNFY.ES..TSS.SQ.QVD.WR.EN.N
Retrocopy AGRDLRTR-PVVRQVRPLIDWDHVKAEGAAWAKRKWADLPPIKKNFYVESTATSSLSQVQVDAWRQENFN

Parental  IMCDDLKGGEKRPIPNPTCQFEDAFQCYPEVMENIQKAGFQKPTPIQSQAWPIVLQGIDLIGVAQTGTGK
          I.C.DLK.GEKRPIPNPTC.FEDAF..YPEV...I.KAGFQ.PTPIQSQAWPIVLQG.DLIGVAQTGTGK
Retrocopy ITCEDLKDGEKRPIPNPTCKFEDAFEHYPEVLKSIKKAGFQRPTPIQSQAWPIVLQGMDLIGVAQTGTGK

Parental  TLSYLMPGFIHLDSQPIAREKRNGPGMLVLTPTRELALQVEAECSKYSYKGLKSVCIYGGGDRNGQIQDL
          TLSYL.PGFIHLDSQPI.RE.RNGPGMLVLTPTRELALQVEAECSKYSYKGLKSVC.YGGG.R..QIQ..
Retrocopy TLSYLIPGFIHLDSQPISREERNGPGMLVLTPTRELALQVEAECSKYSYKGLKSVCVYGGGNRKEQIQHI

Parental  TKGVDIIIATPGRLNDLQMNNFVNLKSVTYLVLDEADKMLDMGFEPQIMKILLDVRPDRQTVMTSATWPY
          TKGVDIIIATPGRLNDLQMN..VNL.S.TYLVLDEADKMLD.GFE.QI.KILLDVRPDRQTVMTSATWP.
Retrocopy TKGVDIIIATPGRLNDLQMNKCVNLRSITYLVLDEADKMLDLGFEGQITKILLDVRPDRQTVMTSATWPH

Parental  SVRRLAQSYLKEPMIVYVGTLDLVAVSTVKQNIIVTTEEEKRSHIQTFLESMSPKDKVIVFVSRKAVADH
          ..R.LA.SYLKEPMIVYVGTLDLVAV.TVKQ.IIVTTEEEKR..IQ.FL....P.DK.I.FVSRK.VAD.
Retrocopy TIRQLARSYLKEPMIVYVGTLDLVAVHTVKQDIIVTTEEEKRTLIQEFLRNLAPEDKAIIFVSRKLVADD

Parental  LSSDLILQHISVESLHGNREQSDRERALENFKTGKVRILIATDLASRGLDVHDVTHVYNYDFPRNIEEYV
          LSSDL..Q...V.SLHGNREQ.DRE.AL..F..G.V.ILIATDLA.RGLDV.DVTHVYNYD.P.N.EEYV
Retrocopy LSSDLSIQGVPVQSLHGNREQFDREQALDDFRSGRVKILIATDLAARGLDVRDVTHVYNYDSPKNLEEYV

Parental  HRVGRTGRAGRTGVSITLLTRNDWRVANELINILERANQSIPEDLVSMAERYKANKLKKEMEKKLGRPQG
          HRVGRTGRAG.TGVS.TL.T..DW..A.ELI.ILERANQS.PEDL..MAE..K..K.KK........PQG
Retrocopy HRVGRTGRAGKTGVSVTLMTQADWKIATELIKILERANQSVPEDLLKMAEQCKLQKGKKDSGNGARNPQG

Parental  KPKKFY
          K.K.FY
Retrocopy KAKQFY

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	0.00 RPM
SRP021940_cerebellum	0.00 RPM	0.00 RPM
SRP021940_embryo	0.00 RPM	0.43 RPM
SRP021940_placental_villous	0.00 RPM	0.43 RPM
SRP021940_synovial_membrane	0.00 RPM	0.44 RPM
SRP021940_testis	1.92 RPM	24.30 RPM

ChIP-Seq

Equus caballus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ecab_7 retrocopy.

TSS

Equus caballus was not studied using FANTOM5 data.

Lab

retro_ecab_7 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ecab_7 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Gorilla gorilla	retro_ggor_2889

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Parental genes homology:

Parental genes homology involve 15 parental genes, and 17 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000007851	1 retrocopy	retro_amel_31,
Callithrix jacchus	ENSCJAG00000009966	2 retrocopies	retro_cjac_3639, retro_cjac_3640,
Equus caballus	ENSECAG00000017971	1 retrocopy	retro_ecab_7 ,
Felis catus	ENSFCAG00000031631	1 retrocopy	retro_fcat_583,
Homo sapiens	ENSG00000080007	1 retrocopy	retro_hsap_76,
Gorilla gorilla	ENSGGOG00000016092	1 retrocopy	retro_ggor_2889,
Microcebus murinus	ENSMICG00000017145	1 retrocopy	retro_mmur_1603,
Monodelphis domestica	ENSMODG00000018546	1 retrocopy	retro_mdom_14,
Mustela putorius furo	ENSMPUG00000004342	1 retrocopy	retro_mputfur_47,
Nomascus leucogenys	ENSNLEG00000001209	1 retrocopy	retro_nleu_1094,
Oryctolagus cuniculus	ENSOCUG00000006338	2 retrocopies	retro_ocun_1061, retro_ocun_227,
Otolemur garnettii	ENSOGAG00000013660	1 retrocopy	retro_ogar_227,
Procavia capensis	ENSPCAG00000005962	1 retrocopy	retro_pcap_151,
Pongo abelii	ENSPPYG00000016774	1 retrocopy	retro_pabe_39,
Pan troglodytes	ENSPTRG00000018344	1 retrocopy	retro_ptro_35,