RetrogeneDB ID: retro_amel_1808

Retrocopy location

• Organism: Panda (Ailuropoda melanoleuca)
• Coordinates: GL194495.1:185793..186463(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSAMEG00000000279
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: SLC7A6OS
• Ensembl ID: ENSAMEG00000007958
• Aliases: None
• Description: solute carrier family 7, member 6 opposite strand [Source:HGNC Symbol;Acc:25807]

Sequence

>retro_amel_1808
GGCACCCAGCAGCATATCCCGCCCGACCTCTGTGCTTTGGCTCAGGAGATCCGGCTGGAAGGCCACTGCAGGGTGGTCTC
TAGCCACCGATCCTGGGGATTCCCTCCAGTGGCCTGGAGTCTGATGTTGCATGGGGAACCCCGAAGCCACACTTCCAGCT
GTTGACCTGGTCCACAAGTAGGGAGACCCAGAGGCCACCTTCAACGGCTCCTGCAAGACATCTGACCCAGAAGTAGTCCT
CTGCAATTTCCCAGAGTTGACCCACAAGCAGCTGACTGTATCCGAGGATGGATCAAGTGTTGGGCACCAGAAGGAACAGA
AGGACAACTCTGTGTACGACATTTACTACGTGGAGATGGCCTCTCCAGGATGGCTGGAGGACTTCCTCTGTGCAGCCCTC
AGCCAGGAGTGGAAGCTGGTGAGTGATGGCTAGCAATCAGAGGACATTTAAGAAGATGAAAATGATGAGAACAAGTGAGA
ATAACTGGCACAATGAGGGCCCAGAGGAGGCGAATAATGCCGGAAATGGAGAAGATTCCAGAGCTCGGATGACTAGGACA
GCGTCAGGGAAAAGGAAGGAGGCAATGGCAGACCAGAGATGTGGAACAAATCCCCTTTGGGGGTGCAGAAGGAGTTTGGC
TATGACAACCCGTCTGACTTGGATTCAGAC

Alignment

ORF - retro_amel_1808 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 59.4 %
• Parental protein coverage: 73.79 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  GSQQRIRRDLRASAREIRQEGRYRVISSRRS-SGIPSSGLESEDA-PGNPEAAEDAGFQLLDLVHEEGDP
          G.QQ.I..DL.A.A.EIR.EG..RV.SS.RS..GIPSSGLES..A..GNP.....A.....DLVH..GDP
Retrocopy GTQQHIPPDLCALAQEIRLEGHCRVVSSHRS<LGIPSSGLESDVA<MGNP----EATLPAVDLVHK*GDP

Parental  EALATAGSPKTSDSDVILCNSVELIRERLTLSEDGPRIGHQEEQKDDYVYDIYYLEMATPGWIENILSVQ
          EA....GS.KTSD..V.LCN..EL....LT.SEDG...GHQ.EQKD..VYDIYY.EMA.PGW.E..L...
Retrocopy EATFN-GSCKTSDPEVVLCNFPELTHKQLTVSEDGSSVGHQKEQKDNSVYDIYYVEMASPGWLEDFLCA-

Parental  PYCQEWELVNDDQQPEDIYEDDDDEN-SETNWRNEYPEEENT--DGDESR-GSDEYDSLSEEERGNSRPE
          ...QEW.LV.D..Q.EDI.ED..DEN.SE.NW.NE.PEE.N....G..SR..SD..DS..E.E.GN.RPE
Retrocopy ALSQEWKLVSDG*QSEDI*EDENDEN>SENNWHNEGPEEANNAGNGEDSR<SSDD*DSVREKEGGNGRPE

Parental  MWSKYPLDVQKEFGYDSPHDLDSD
          MW.K.PL.VQKEFGYD.P.DLDSD
Retrocopy MWNKSPLGVQKEFGYDNPSDLDSD

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_1808 retrocopy.

TSS

Ailuropoda melanoleuca was not studied using FANTOM5 data.

Lab

retro_amel_1808 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 3 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000007958	1 retrocopy	retro_amel_1808 ,
Macropus eugenii	ENSMEUG00000003614	6 retrocopies	retro_meug_1263, retro_meug_1647, retro_meug_1823, retro_meug_849, retro_meug_884, retro_meug_979,
Myotis lucifugus	ENSMLUG00000005953	1 retrocopy	retro_mluc_346,