RetrogeneDB ID: retro_amel_350

Retrocopy location

• Organism: Panda (Ailuropoda melanoleuca)
• Coordinates: GL192395.1:1961206..1961691(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSAMEG00000015139
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: YRDC
• Ensembl ID: ENSAMEG00000001173
• Aliases: None
• Description: yrdC domain containing (E. coli) [Source:HGNC Symbol;Acc:28905]

Sequence

>retro_amel_350
ACACTGTATGGCCTGACCTGCTCGGCCAGCTGGGCACTGTGTACTGCCTCCAGGGCTGCAGCCACTCCAAGCTGCCGGCC
TTCTGCCTGAGCTGCGTGGCTGACGTCTTCAGGTACTGCCACGTGAGAGTACCCGCGGGGCTCCTGAAAGACTTACTACC
AAGACCAGTGACCCTGGTATTGGAACACTCCCAGGAGCTCAGTAAGGACCTGAACCTCTTTCCTTCTCTTACAGGCATCT
GGATTCCTGACCCTGCCTTCAAGCAGGACTTGGCTCAGGTGTTTGGGGCACCATTTGCTCTCATAAGTGCCAACCTCAGC
TCTCAGGCCAGTTCTCAGAATGTCTTTGAATTCCAGAACCTCTGGCCTCAACTATCCCTGGTTATTGATGGGGGACCAAC
AGAGGATGGCCAGGGTCCTGAGTATCACCTGGGCTCAACTACGGCTGACTTGTCTGTATCTGGAAAGTTTGGCATCATTC
ATCCT

Alignment

ORF - retro_amel_350 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 71.86 %
• Parental protein coverage: 88.3 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  TLYGLACSASCSEA-LGAVYRLKGRSEAKPLAVCLGRVADVYRYCHVRVPEGLLKDLLPGPVTLVLERSE
          TLYGL.....CS...LG.VY.L.G.S..K..A.CL..VADV.RYCHVRVP.GLLKDLLP.PVTLVLE.S.
Retrocopy TLYGL----TCSAS<LGTVYCLQGCSHSKLPAFCLSCVADVFRYCHVRVPAGLLKDLLPRPVTLVLEHSQ

Parental  ELNKDLNPFTPLVGIRIPDHAFIQDLVQVFGGPLALTSANLSSQASSLNVEEFQDLWPQLSLVIDGGPIG
          EL.KDLN.F..L.GI.IPD.AF.QDL.QVFG.P.AL.SANLSSQASS.NV.EFQ.LWPQLSLVIDGGP..
Retrocopy ELSKDLNLFPSLTGIWIPDPAFKQDLAQVFGAPFALISANLSSQASSQNVFEFQNLWPQLSLVIDGGPTE

Parental  DGQSPEYRLGSTVVDLSVPGKFGIIRP
          DGQ.PEY.LGST..DLSV.GKFGII.P
Retrocopy DGQGPEYHLGSTTADLSVSGKFGIIHP

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_350 retrocopy.

TSS

Ailuropoda melanoleuca was not studied using FANTOM5 data.

Lab

retro_amel_350 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 16 parental genes, and 26 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000001173	1 retrocopy	retro_amel_350 ,
Dasypus novemcinctus	ENSDNOG00000009111	2 retrocopies	retro_dnov_1774, retro_dnov_2232,
Equus caballus	ENSECAG00000022522	1 retrocopy	retro_ecab_534,
Felis catus	ENSFCAG00000011018	1 retrocopy	retro_fcat_375,
Homo sapiens	ENSG00000196449	2 retrocopies	retro_hsap_4199, retro_hsap_4289,
Gorilla gorilla	ENSGGOG00000007619	1 retrocopy	retro_ggor_2866,
Macropus eugenii	ENSMEUG00000005068	1 retrocopy	retro_meug_452,
Microcebus murinus	ENSMICG00000011953	1 retrocopy	retro_mmur_188,
Myotis lucifugus	ENSMLUG00000000955	1 retrocopy	retro_mluc_367,
Macaca mulatta	ENSMMUG00000005372	2 retrocopies	retro_mmul_1206, retro_mmul_1662,
Nomascus leucogenys	ENSNLEG00000011665	2 retrocopies	retro_nleu_1045, retro_nleu_1046,
Otolemur garnettii	ENSOGAG00000030474	2 retrocopies	retro_ogar_1107, retro_ogar_2342,
Pongo abelii	ENSPPYG00000001523	1 retrocopy	retro_pabe_3495,
Pan troglodytes	ENSPTRG00000000557	4 retrocopies	retro_ptro_2850, retro_ptro_2906, retro_ptro_2907, retro_ptro_2999,
Tupaia belangeri	ENSTBEG00000008863	1 retrocopy	retro_tbel_1817,
Tarsius syrichta	ENSTSYG00000005555	3 retrocopies	retro_tsyr_1108, retro_tsyr_1420, retro_tsyr_874,