RetrogeneDB ID: retro_amel_778

Retrocopy location

• Organism: Panda (Ailuropoda melanoleuca)
• Coordinates: GL192627.1:1425678..1426301(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSAMEG00000004134
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSAMEG00000001020
• Aliases: None
• Description: None

Sequence

>retro_amel_778
CCTTACAGTGCCGTCTCCTTTCCTGTTCGAGGGCGACGAGATGCCATGTGCATGCTGCTGGCTGACCAGGGCCAGAGCTG
GAAGGAAGACATGGTGACCAAGGAGACCTGGCTGCAGAGCGCACTCAAGGCCTCCTGTCTACCCGGGAAGCTTCCCGAGT
TCCAGGAAGGAGACCTTACCCTGTACCAGTCCAGTGCCATCCTGCAATACCTGGGCCACTCCCTTGGGCTCTATTGGAAG
AACCAGTGGGAGGCCACCCTGGTGGATGTTGTGAATGACCGCGTGAAGAATCTCCACTGCAAATACCTCATTCTTACCTA
TGTCAACCACAAGGCAGGCAAGGAGGGGTATATGAAAGCACGACCGGGGCACCTGAAGCCATTTGAGATCCTGCTGTCCT
AGACCGGGAGGGGCAGGTCTTAATCGTAGGCAGCTCGGTCTCCTTCTTGGACTACACCTTGCTGAACTGGCTGCTGATTC
ACCAGGTCCTGGCCCCCAGCTGCCTGGACTCCTTCCCCCTGCTCTCTGCCTGTGTGGTGTGCCTCAGCCCCGGGCCCAAG
CTCAAGTCCTTCCTGGCCTTCCCCTAGCGTATGAAGCTCCCCACCAACTACAACAGGAAGCGG

Alignment

ORF - retro_amel_778 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 66.99 %
• Parental protein coverage: 99.05 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  PYTIVYFPVRGRCEAMRMLLADQGQSWKEEVVTKETWLQGPLKASCLYGQLPKFQDGDLTLYQSNAILRH
          PY..V.FPVRGR..AM.MLLADQGQSWKE..VTKETWLQ..LKASCL.G.LP.FQ.GDLTLYQS.AIL..
Retrocopy PYSAVSFPVRGRRDAMCMLLADQGQSWKEDMVTKETWLQSALKASCLPGKLPEFQEGDLTLYQSSAILQY

Parental  LGRSLGLYGKDQREAALLDVVNDGVEDLRCKYVMLIYTNYEAGKEEYLKALPGYLKPFETLLS-QNEGGQ
          LG.SLGLY.K.Q.EA.L.DVVND.V..L.CKY..L.Y.N..AGKE.Y.KA.PG.LKPFE.LLS.....GQ
Retrocopy LGHSLGLYWKNQWEATLVDVVNDRVKNLHCKYLILTYVNHKAGKEGYMKARPGHLKPFEILLS<LDREGQ

Parental  AFIVGNQISFADYNLLDLLLIHQVLAPSCLDSLPLLSAYVARLSARPKLKAFLASPEHVNRPINGNGKQ
          ..IVG...SF.DY.LL..LLIHQVLAPSCLDS.PLLSA.V..LS..PKLK.FLA.P.....P.N.N.K.
Retrocopy VLIVGSSVSFLDYTLLNWLLIHQVLAPSCLDSFPLLSACVVCLSPGPKLKSFLAFP*RMKLPTNYNRKR

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_778 retrocopy.

TSS

Ailuropoda melanoleuca was not studied using FANTOM5 data.

Lab

retro_amel_778 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 13 parental genes, and 31 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000001020	3 retrocopies	retro_amel_1921, retro_amel_249, retro_amel_778 ,
Ailuropoda melanoleuca	ENSAMEG00000004970	1 retrocopy	retro_amel_1548,
Canis familiaris	ENSCAFG00000011349	4 retrocopies	retro_cfam_143, retro_cfam_2043, retro_cfam_46, retro_cfam_617,
Callithrix jacchus	ENSCJAG00000000879	1 retrocopy	retro_cjac_3321,
Macropus eugenii	ENSMEUG00000001519	2 retrocopies	retro_meug_1519, retro_meug_1762,
Myotis lucifugus	ENSMLUG00000011529	4 retrocopies	retro_mluc_1669, retro_mluc_1714, retro_mluc_1962, retro_mluc_629,
Mustela putorius furo	ENSMPUG00000004029	2 retrocopies	retro_mputfur_1215, retro_mputfur_1463,
Mus musculus	ENSMUSG00000038155	1 retrocopy	retro_mmus_521,
Oryctolagus cuniculus	ENSOCUG00000002230	1 retrocopy	retro_ocun_391,
Pteropus vampyrus	ENSPVAG00000008586	6 retrocopies	retro_pvam_1119, retro_pvam_1463, retro_pvam_568, retro_pvam_664, retro_pvam_681, retro_pvam_718,
Rattus norvegicus	ENSRNOG00000018237	4 retrocopies	retro_rnor_2140, retro_rnor_2567, retro_rnor_2842, retro_rnor_769,
Tursiops truncatus	ENSTTRG00000003746	1 retrocopy	retro_ttru_1416,
Vicugna pacos	ENSVPAG00000008003	1 retrocopy	retro_vpac_73,