RetrogeneDB ID: retro_amel_1473

Retrocopy location

• Organism: Panda (Ailuropoda melanoleuca)
• Coordinates: GL193458.1:182601..183360(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSAMEG00000002288
• Aliases: None
• Description: None

Sequence

>retro_amel_1473
TCTGGTGAGACGATGGGCACTCTGCAGACCAACTGGTCACTGCCTTTGCTTTTTCTGACTGAAATAGGATGAGTATGTAC
TTAGTTTCCACAGCCTGAACATAAGGACCCAGGATGAAGGACTCCTTTCCCAAGTTGTATCCTAAAGAGTACCAAGAAGA
AATACAGTTACCAAAGATAATTGCGTTCATCCTTTCTCCGTGGAGCAGATGGCCAAACAAAAACCCGCATTCATCAAGCC
CTGTGGTACAGCAACAGCTGCAAATTATTCTTTCCTGACCGATGGTGAATCAGCAGTGCTGATTATGGCAGAGGAAAAAG
CTCTGGCCACGGGTTATAAATGGAGGACATTTTTGAGGGATTTTGTGTAAGTATCTCAGGATCCAAAAGATCAACTTTTA
CTCAGGCAACATATGCTATTCCAGAAGTTTTGGAGAAGGCAGGATTAACTGGTATTGATGCTTTTGAATTTCAGGAAGTT
TTCTCAGGTCAGATTTTGGCTAATTTGAAAGCCATGGATTCTGATTTGTTTGCACAAAAATACATGGTTAGGAAAACCAA
GGTTGGATTGCCTACTTTAAAGAAGTTTAACAACTAGGGTGGATGTCTGTTCCTGAGATACCCATTTGGAGCCACTGGCT
GCAGGTTGGTCATGGAACCTTTCAACAGATTACAGAAGGAAGGAGGCCAGTATTCCCTAGTGAGTGCCTATACAGGTAGA
GAGCAGGACCATGCTATGATAGTAGAAGCTTATGAAAAA

Alignment

ORF - retro_amel_1473 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 69.88 %
• Parental protein coverage: 53.89 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  TSETMG-HSADRLAAAFAVSRQDQ-DEYALSSHSLAKKAQDEGLLSDVVPFKVPGKDTVTKDNGIRPSSL
          ..ETMG.HSAD.L..AFA.S.....DEY.LS.HSL....QDEGLLS.VV...VP...TVTKDN...P.S.
Retrocopy SGETMG<HSADQLVTAFAFSD*NR<DEYVLSFHSLNIRTQDEGLLSQVVS*RVPRRNTVTKDNCVHPFSV

Parental  EQMAKLKPAFIKPYGTVTAANSSFLTDGASAMLIMAEEKALAMGYKPKAYLRDFVYVSQDPKDQLLL-GP
          EQMAK.KPAFIKP.GT.TAAN.SFLTDG.SA.LIMAEEKALA.GYK....LRDFV.VSQDPKDQLLL...
Retrocopy EQMAKQKPAFIKPCGTATAANYSFLTDGESAVLIMAEEKALATGYKWRTFLRDFV*VSQDPKDQLLL<QA

Parental  TYATPKVLEKAGLTMNDIDAFEFHEAFSGQILANFKAMDSDWFAQNYMGRKTKVGSPPLEKFNNWGGSLS
          TYA.P.VLEKAGLT...IDAFEF.E.FSGQILAN.KAMDSD.FAQ.YM.RKTKVG.P.L.KFNN.GG.L.
Retrocopy TYAIPEVLEKAGLT--GIDAFEFQEVFSGQILANLKAMDSDLFAQKYMVRKTKVGLPTLKKFNN*GGCLF

Parental  LGHPFGATGCWLVMAAANRLRKEGGQYGLVAACAAGGQGHAMIVEAYPK
          L..PFGATGC.LVM...NRL.KEGGQY.LV.A.....Q.HAMIVEAY.K
Retrocopy LRYPFGATGCRLVMEPFNRLQKEGGQYSLVSAYTGREQDHAMIVEAYEK

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_1473 retrocopy.

TSS

Ailuropoda melanoleuca was not studied using FANTOM5 data.

Lab

retro_amel_1473 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 11 parental genes, and 15 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000002288	1 retrocopy	retro_amel_1473 ,
Canis familiaris	ENSCAFG00000029395	1 retrocopy	retro_cfam_2114,
Choloepus hoffmanni	ENSCHOG00000010050	3 retrocopies	retro_chof_122, retro_chof_1869, retro_chof_911,
Homo sapiens	ENSG00000138029	1 retrocopy	retro_hsap_4778,
Gorilla gorilla	ENSGGOG00000025829	1 retrocopy	retro_ggor_2976,
Microcebus murinus	ENSMICG00000006750	1 retrocopy	retro_mmur_1315,
Mus musculus	ENSMUSG00000059447	2 retrocopies	retro_mmus_1427, retro_mmus_1961,
Otolemur garnettii	ENSOGAG00000005444	1 retrocopy	retro_ogar_167,
Pongo abelii	ENSPPYG00000012582	1 retrocopy	retro_pabe_3718,
Pan troglodytes	ENSPTRG00000011733	1 retrocopy	retro_ptro_3180,
Tarsius syrichta	ENSTSYG00000003570	2 retrocopies	retro_tsyr_1316, retro_tsyr_1951,