RetrogeneDB ID: retro_amel_31

Retrocopy location

• Organism: Panda (Ailuropoda melanoleuca)
• Coordinates: GL194402.1:154403..156236(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSAMEG00000019953
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: DDX43
• Ensembl ID: ENSAMEG00000007851
• Aliases: None
• Description: DEAD (Asp-Glu-Ala-Asp) box polypeptide 43 [Source:HGNC Symbol;Acc:18677]

Sequence

>retro_amel_31
GGCGGCGGCAGCAGCAGAAGGGGCGGAAGCGGCAGAGGCTGGAGCGCTCCCTCCGGCTCCATGGAGCTTAGAGCCTCAGG
CCCCAGAGAACCACCTCTCTGCTTTAGACTGAGGAGCAATATGATTGGTGTGGTGATTGGTCGTGGTGGATCAAAGATAA
AAGACATCCAGGCTATGACAAACACCAAAATACAGATCATAAAAGGTGATTCTGAAGCAGAGGTAAAAATTTTTGGCGCC
ACGGACATGAAAGCAAAGGCCAAAGCAGCTATAGATGCTCTTGTTAAAAAACAAGAACGAGGCCACCATTCAGAGTCCCG
TGTGGATAGTGCCACACCTCAGGCCTCTGCTGGAAGAGAGTTTCGCCCAGATAACACTGGCGGTAGGCAAGTTCAGTCAC
TGATAGATTGGGATCAAATTAGGGCAGAAGTTGTAGAGTGGGAAAAAAGAAAATGGGCATATTTACCACCAATTAAGAAA
AACTTTTACGTAGAATCTGAAGCAACCAGCTCATTGTCTCAAGTTCAGGTAGACATGTGGAGAAAGGAAAATTTTGACCT
AATATGTGACGACTTGAAAGATGGTGAAAAGCGCCCCATCCCCAATCCTACTCGTCTGTTTGAGGATGCTTTCCATCCTT
ATCCTGAACTTATTGAAAGCATTAAAAGAGCAGGTTTTCAAAAGCCAACGCCAATTCAGTCACAGGCGTGGCCAATTATT
CTACAAGGAATAGATCTTATAGGAGTTGCGCAAACCGGAACGGGCAAAACTTTGTCCTATTTAATGCCTGGGTTTATCCA
CCTCAATAATCAACCAATATCCAGAGAGGAAAGGAATGGACCTGGCATGCTAGTCCTTACACCCACTAGAGAATTAGCTC
TTCAGGTGGAAGCTGAATGTTCTAAGTATTCATATAAAGGTCTTAAAAGTATTTGTATATTTGGTGGCAGAAATAGAGAA
CAACAAATACGAGACATTACCAAAGGCATAGATATCATTATTGCAACTCCTGGACGACTAAATTATCTGCAAATGAATAA
CTTTGTCAACTTACAAAGCATAACCTACTTAGTCTTAGATGAAGCAGATAAAATGCTAGATCTGGGGTTTGAACACCAGA
TAATGAAGATTTTATTAGATGTGCGCCCAGACCGCCAGACTGTTATGATAAGTGCAACTTGGTCAGATACCATTCATCAG
CTTGGTCAGTCTTATTTGAAAGAGCCTATGATTGTTTATGTTGGTACTCTGGATCTAGTTGCTGTTAATACTGTGACGCA
AAATGTGATCATTACCACACAAGAAGAAAAACGATCTCTTCTCCAAGAATTCCTGCAGAACCGTTCACCCCAAGACAAAG
TCATCGTGTTTGTCAGAAGAAGACTTGTTGCTGATGACTTATCAAGTGATTTGAGCATCCAAGGCATAACAGTGCAGTCA
CTACATGGCGACAGAGACCAGCATGATCGTGAACGAGCATTGGAGGACTTCAGAAGTGGAAAAGTGAAAGTACTGATTGC
TACTGATTTAGCATCCAGAGGTCTTGATGTTAATGATATCACACACGTATATAATTACGACTTCCCGCGCAATATTGAAG
AATATGTACACAGAGTGGGGCGAACTGGAAGAGCAGGGAAGACTGGTTTATCAATTACCCTCATGACTCAAAATGATTGG
AAGATCGCCACTGAATTGATTAAAATTCTGAAACGAGCAAATCAGAGTGTCCCTGAAGATCTTCTAACAATGGCCGAGCA
ATACAAATTGCATAAACAAAAAAAGGACACAGGAAAAAGAAAATCTCAAGGAAAATCCAGGGAGTTTTATTGA

Alignment

ORF - retro_amel_31 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 69.87 %
• Parental protein coverage: 94.15 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  GQEARRGGRGGGWTNPSGLQQPVAPGLREPPLCFGLKNAWVGAVIEIGRGGSKIKDIQSTTNTKIQITKG
          G...RRGG.G.GW..PSG.....A.G.REPPLCF.L.....G.VI..GRGGSKIKDIQ..TNTKIQI.KG
Retrocopy GGSSRRGGSGRGWSAPSGSMELRASGPREPPLCFRLRSNMIGVVI--GRGGSKIKDIQAMTNTKIQIIKG

Parental  HLEEAEVRIFGSKVMQAKAKTVIDNLVKKQEN-YSSKLRTDIGAFQPSVGRDVKTDNNVTEN-QPLIDWD
          ...EAEV.IFG...M.AKAK..ID.LVKKQE....S..R.D....Q.S.GR....DN......Q.LIDWD
Retrocopy D-SEAEVKIFGATDMKAKAKAAIDALVKKQERGHHSESRVDSATPQASAGREFRPDNTGGRQVQSLIDWD

Parental  QIREDALKWGKKKWEDLPPIKKNFYVESEATSTMSQVQVDNWRKENYNIMCDDLKENEKRSIPNPTCKFE
          QIR.....W.K.KW..LPPIKKNFYVESEATS..SQVQVD.WRKEN....CDDLK..EKR.IPNPT..FE
Retrocopy QIRAEVVEWEKRKWAYLPPIKKNFYVESEATSSLSQVQVDMWRKENFDLICDDLKDGEKRPIPNPTRLFE

Parental  DAFQRYPEVMENIKKAGFQKPTPIQSQSWPIVLQGIDLIGVAQTGTGKTLSYLMPGFIHLDSQPVIRGQR
          DAF..YPE..E.IK.AGFQKPTPIQSQ.WPI.LQGIDLIGVAQTGTGKTLSYLMPGFIHL..QP..R..R
Retrocopy DAFHPYPELIESIKRAGFQKPTPIQSQAWPIILQGIDLIGVAQTGTGKTLSYLMPGFIHLNNQPISREER

Parental  NGPGMLVLTPTRELALQVEAECSKYSYKGLKSVCIYGGGDRNGQIQDLKKGVDIIIATPGRLNDLQMNNF
          NGPGMLVLTPTRELALQVEAECSKYSYKGLKS.CI.GG..R..QI.D..KG.DIIIATPGRLN.LQMNNF
Retrocopy NGPGMLVLTPTRELALQVEAECSKYSYKGLKSICIFGGRNREQQIRDITKGIDIIIATPGRLNYLQMNNF

Parental  VNLRSVTYLVLDEADKMLDMGFEPQIMKILLDVRPDRQTIMTSATWPYAVRRLAQSYLKEPMIVYVGTLD
          VNL.S.TYLVLDEADKMLD.GFE.QIMKILLDVRPDRQT.M.SATW......L.QSYLKEPMIVYVGTLD
Retrocopy VNLQSITYLVLDEADKMLDLGFEHQIMKILLDVRPDRQTVMISATWSDTIHQLGQSYLKEPMIVYVGTLD

Parental  LMAVSTVKQNIIVTTEEEKCSHIQTFLESMSPKDKVIVFVSRKATADHLSSDLILRHVSVESLHGNREQS
          L.AV.TV.QN.I.TT.EEK.S..Q.FL...SP.DKVIVFV.R...AD.LSSDL......V.SLHG.R.Q.
Retrocopy LVAVNTVTQNVIITTQEEKRSLLQEFLQNRSPQDKVIVFVRRRLVADDLSSDLSIQGITVQSLHGDRDQH

Parental  DRERALENFKTGKVRILIATDLASRGLDVLDITHVYNYDFPRNIEEYVHRVGRTGRAGRTGISITLLTRN
          DRERALE.F..GKV..LIATDLASRGLDV.DITHVYNYDFPRNIEEYVHRVGRTGRAG.TG.SITL.T.N
Retrocopy DRERALEDFRSGKVKVLIATDLASRGLDVNDITHVYNYDFPRNIEEYVHRVGRTGRAGKTGLSITLMTQN

Parental  DWRVAGELINILERAQQSIPEDLVAMAKRYEANKLKKEMEEKLGKPQGKPQRFY
          DW..A.ELI.IL.RA.QS.PEDL..MA..Y...K.KK.......K.QGK...FY
Retrocopy DWKIATELIKILKRANQSVPEDLLTMAEQYKLHKQKKDTGKR--KSQGKSREFY

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Ailuropoda melanoleuca was not studied using RNA-Seq expression data.

ChIP-Seq

Ailuropoda melanoleuca was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_amel_31 retrocopy.

TSS

Ailuropoda melanoleuca was not studied using FANTOM5 data.

Lab

retro_amel_31 was not experimentally validated.

Homology

Retrocopy orthology:

Ailuropoda melanoleuca does not belong to any of the species groups (eutheria, teleost or neognath), studied for retrocopy-based homology. For more information about studied groups, please go to help section.

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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,