RetrogeneDB ID: retro_amel_1135

Retrocopy location

• Organism: Panda (Ailuropoda melanoleuca)
• Coordinates: GL192942.1:501210..501456(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SEPW1
• Ensembl ID: ENSAMEG00000015208
• Aliases: None
• Description: selenoprotein W, 1 [Source:HGNC Symbol;Acc:10752]

Sequence

>retro_amel_1135
CAAATCGTTTACTGTGGTACCTGAGGCTACAAGTCCAAGCATCTTCAGCTCAAGAGGAAGTTAGAAGATGAGTTCCCCAG
ATGCCTGGACATCTATGGTGAGAGGACTCCATAGGCCATTGGCTTCTTTGAAGTGATGGTAGCAGGGAAGTTGGTTCACT
CCAAGAAGAGAGGTGATGGCTACATGGACACAGAGAGCAAGTTTCTGAAGCTGTTGGCCACCATCAAAGCCACCTTGGCT
CAGGGC

Alignment

ORF - retro_amel_1135 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 80.49 %
• Parental protein coverage: 94.25 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  RVVYWGWWGYKSKYLQLKKKLEDEFPGCLDICGEGTPQATGFFEVMVAGKLVHSKKRGDGYVDTESKFLK
          ..VY.G..GYKSK.LQLK.KLEDEFP.CLDI.GE.TP.A.GFFEVMVAGKLVHSKKRGDGY.DTESKFLK
Retrocopy QIVYCGT*GYKSKHLQLKRKLEDEFPRCLDIYGERTP*AIGFFEVMVAGKLVHSKKRGDGYMDTESKFLK

Parental  LVAAIKAALAQG
          L.A.IKA.LAQG
Retrocopy LLATIKATLAQG

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_1135 retrocopy.

TSS

Ailuropoda melanoleuca was not studied using FANTOM5 data.

Lab

retro_amel_1135 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 8 parental genes, and 12 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000015208	1 retrocopy	retro_amel_1135 ,
Bos taurus	ENSBTAG00000008203	2 retrocopies	retro_btau_1527, retro_btau_756,
Canis familiaris	ENSCAFG00000004074	1 retrocopy	retro_cfam_1368,
Choloepus hoffmanni	ENSCHOG00000013206	2 retrocopies	retro_chof_1486, retro_chof_61,
Felis catus	ENSFCAG00000015176	2 retrocopies	retro_fcat_108, retro_fcat_186,
Mustela putorius furo	ENSMPUG00000004433	1 retrocopy	retro_mputfur_326,
Rattus norvegicus	ENSRNOG00000013548	2 retrocopies	retro_rnor_1819, retro_rnor_688,
Ictidomys tridecemlineatus	ENSSTOG00000001294	1 retrocopy	retro_itri_578,