RetrogeneDB ID: retro_amel_46

Retrocopy location

• Organism: Panda (Ailuropoda melanoleuca)
• Coordinates: GL193784.1:133505..135263(-)
• Located in intron of: ENSAMEG00000017536

Retrocopy information

• Ensembl ID: ENSAMEG00000019173
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSAMEG00000016012
• Aliases: None
• Description: None

Sequence

>retro_amel_46
GAGGGTCAAAGTGATAAGACCGAGGATGCCAACATTGTGGTCAAGAGAAAGAGTGCTACACTGCACGACCAGAGTTCTCC
AACCGTCTATGGGGAGGGTATCCAGGGCCTCCCGGGAAAACTGATGGCAGAAGGCGACGAAGGCACTAGTGTAAAACCCA
GCCCAAGAGAGCATCTCAACCCGGGCCAAAGACCTGCCAGGGTCGTCACCTTCTCTGCTCCTCAGAACAAGCAGCTGGTA
GCCCCCGAGGTTAGAGTGAAGGAAAAGATAGCGATAGAGGTCAACAGCTCTGGTAACAGGCGGGTGATTATTGATCCGCT
GGAGAAAACCTGTCAGAAGCCACCTAGCGACCAAAGGGTGGTCATTTTTGAAAAAGGCTCTCCACCCCTAACATTTCTAG
ACAAATGTGACCCTTACTCAGAAATGCAAAAGTATCAAGAAAGGGAGGCCATGGCTGAGCACCCCTACTCAGCAAGTTAC
CTGCCTGGTATGGAAGAGCTATCTGCATTGGAATTCCCTCAGGAGGAGCCAATCTCCCTGGGTCTCTCATTAGTTCCCAA
GCCTTCACCCTTCCCCGCTGACTGTGTCCTGGACCAGTCTTATTTGTACAGGGATCCCTGGCAGGCCTACACCAGCTACT
GGAGCAGTAGCCCCCAGCCTTCCTACTATCCTTCCGTGGGCCCCGGCAGTGACGGCACATCCCAGGCTGGGAGGGGCAGC
CACAGCTTCTTTAGCAGTTATTCCTCCAGCTCAGAAATGTACTTCCAAAACTGGCCCAGAGACTGGAACGCATTAGAGGA
AGGTTGGTCCCAGAACTTTCACTCCTATCAGTTCCCTAGAAGTCTAGAAGCCCAGGAGCCAACCGTCCAAGAGGAGACCG
TGTCATCATATCCTTTTGGAGGGTACACGTCTCCCTTCTGGCCGAGGAGCCACTGGAGTCGAGGCCTCGATCAGGGTTTC
ATTGATACCCACTGTCACTTGGACATTCTGTACTCCAAGCTGTCTTTCAAAGGGACCTTTAGCAAGTTCACAGAAATGTA
TAACTACTCCTTCCCTAAGGAGTTCCAGGGCTGCATCTCCGATTTCTGTGATCCTCGCGCACTAAGGGATGGCCTGTGGG
AAGAGCTGCTGAAAGATGATCTGGTTTGGGGGGCCTTCGGCTGTCACCCCCATTTTGCACGTTACTACAATGACACTCAA
GAAAGAAAGCTGCTGCAGGCCCTACGGCACCCCAAGGCCATAGCGTTTGGAGAAATGGGCTTGGATTACTCTTACAAGTG
CACCACACCTGTCCCACAGCAGCACAAAGTGTTCGAGAGACAGCTGCAGTTGGCCGTGTCCCTGAAGAAGCCCTTGGTGA
TCCACTGCCGAGAAGCTGACGAAGATCTGCTGGGGATCTTGAAAAGAAGGGTGCCCCCTGACTACAAGATCCACAGGCAC
TGCTTCACGGGCGAATACTCCGTCCTCGAGCCCCTCCTGAAGTATTTTCCCAACATGTCTGTGGGGTTCACAGCGGTCCT
GACCTACTCCTCCGCCTGGGAGACCCGGGATGCTCTGAGAATGATCCCGCTAGACAGAATCGTCGTGGAAACCGATGCGC
CCTACTTCCTGCCTCGTGGGGTTCCCAAAAGCGTTTGCCAGTATACCCACCCGGGCCTGGCCCTATATACGGTTCGCGAG
ATTGCCAGAATCAAAGGTCAGCCGCTCGCCCGCACCCTGGCCATCTTGCGTGAGAACACTAACTACCTCTACAATCTT

Alignment

ORF - retro_amel_46 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 61.89 %
• Parental protein coverage: 79.36 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  EGRNDTNEEPNKVQKRKRDRFRDQGSTVIYLKAIQGILGKSMPKKKGEGATRATPTKGERPSRGEGPARS
          EG..D..E..N.V.KRK.....DQ.S...Y...IQG..GK.M....G...T...P...E....G..PAR.
Retrocopy EGQSDKTEDANIVVKRKSATLHDQSSPTVYGEGIQGLPGKLMAE--GDEGTSVKPSPREHLNPGQRPARV

Parental  VTVSPPQKGKESAPEVRAEDEKPAPERSSFCDRRVVIDPQEKPSEETAGDRRTVV-DKHSPALEFLDDSD
          VT.S.PQ.....APEVR...EK.A.E..S...RRV.IDP.EK.......D.R.V...K.SP.L.FLD..D
Retrocopy VTFSAPQNKQLVAPEVRVK-EKIAIEVNSSGNRRVIIDPLEKTCQKPPSDQRVVIFEKGSPPLTFLDKCD

Parental  SHLESQKPKEREVVIEHTSSGSDWSDVDEVSTVRFSQEEPSSLKLSAVPEPSAFSTDYVMYPAHLYSSPW
          ...E.QK..ERE...EH..S.S......E.S...F.QEEP.SL.LS.VP.PS.F..D.V.....LY..PW
Retrocopy PYSEMQKYQEREAMAEHPYSASYLPGMEELSALEFPQEEPISLGLSLVPKPSPFPADCVLDQSYLYRDPW

Parental  RDYASYWTSSPKPSGYPSVGSSSSSSDPLQAGRSSRGLLSDYSPNSAGSSQNTSRDQEVTEEGRSQNSRS
          ..Y.SYW.SSP.PS.YPSVG..S......QAGR.S....S.YS..S....QN..RD....EEG.SQN..S
Retrocopy QAYTSYWSSSPQPSYYPSVGPGSDGTS--QAGRGSHSFFSSYSSSSEMYFQNWPRDWNALEEGWSQNFHS

Parental  FRFSRSSEEEGKEKRALQEEAPPRPCGGHASSSLPRNHRESGPEEGFIDTHCHLDMLYSKLAFKGSFTKF
          ..F.RS.E....E.....E.....P.GG..S...PR.H...G...GFIDTHCHLD.LYSKL.FKG.F.KF
Retrocopy YQFPRSLEAQ--EPTVQEETVSSYPFGGYTSPFWPRSHWSRGLDQGFIDTHCHLDILYSKLSFKGTFSKF

Parental  RKIYSSSFPKEFQGCISDFCDPRTLTDCLWEELLKEDLVWGAFGCHPHFARYYSESQERNLLQALRHPKA
          ...Y..SFPKEFQGCISDFCDPR.L.D.LWEELLK.DLVWGAFGCHPHFARYY...QER.LLQALRHPKA
Retrocopy TEMYNYSFPKEFQGCISDFCDPRALRDGLWEELLKDDLVWGAFGCHPHFARYYNDTQERKLLQALRHPKA

Parental  VAFGEMGLDYSYKCTTPVPEQHKVFERQLQLAVSLKKPLVIHCREADEDLLNIMKKFVPSDYKIHRHCFT
          .AFGEMGLDYSYKCTTPVP.QHKVFERQLQLAVSLKKPLVIHCREADEDLL.I.K..VP.DYKIHRHCFT
Retrocopy IAFGEMGLDYSYKCTTPVPQQHKVFERQLQLAVSLKKPLVIHCREADEDLLGILKRRVPPDYKIHRHCFT

Parental  GSYPVIEPLLKHFPNMSVGFTAVLTYSSAWEARDALKQIPLERIIVETDAPYFLPRQVPKSLCQYAHPGL
          G.Y.V.EPLLK.FPNMSVGFTAVLTYSSAWE.RDAL..IPL.RI.VETDAPYFLPR.VPKS.CQY.HPGL
Retrocopy GEYSVLEPLLKYFPNMSVGFTAVLTYSSAWETRDALRMIPLDRIVVETDAPYFLPRGVPKSVCQYTHPGL

Parental  ALHTVREIARVKDQPLSHTLAILRENTSRLYNL
          AL.TVREIAR.K.QPL..TLAILRENT..LYNL
Retrocopy ALYTVREIARIKGQPLARTLAILRENTNYLYNL

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_46 retrocopy.

TSS

Ailuropoda melanoleuca was not studied using FANTOM5 data.

Lab

retro_amel_46 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.

---

Parental genes homology:

Parental genes homology involve 5 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000016012	1 retrocopy	retro_amel_46 ,
Canis familiaris	ENSCAFG00000005131	1 retrocopy	retro_cfam_2059,
Equus caballus	ENSECAG00000010589	1 retrocopy	retro_ecab_1057,
Mustela putorius furo	ENSMPUG00000017160	1 retrocopy	retro_mputfur_757,
Otolemur garnettii	ENSOGAG00000017043	1 retrocopy	retro_ogar_819,