RetrogeneDB ID: retro_amel_1301

Retrocopy location

• Organism: Panda (Ailuropoda melanoleuca)
• Coordinates: GL193169.1:489530..490106(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: THEM4
• Ensembl ID: ENSAMEG00000000355
• Aliases: None
• Description: thioesterase superfamily member 4 [Source:HGNC Symbol;Acc:17947]

Sequence

>retro_amel_1301
AGGTAGTTTTCTTCTGAGATCATTAATAGGAACCGTTCTCTCCCATGCCCAGCTGGGGCAAGGACATGAGACTCTTCATT
GACCAGTTCATGAAGAAATGTGAAGATGGCTTCTAGAAACGTTTGCCTTCATATGAATGTAAATCAACTTGAAGTATTAA
AGACTTCAAAACCTTTTTCGTGACGCAAAGCCTGTACAATAACAAATGTCATAGGCCCAGCTCTTCCCTAGAAGCCTTAA
GGAAGGCCTGGGCCTTGAATATGTGATATTCCATAATCATGTTGAAGAAAGGATAGTTTGCATATTTCAAGGAGGTCCTT
ACCTGCAAGGAGCACCTGGATTCCTTCATGGAGCTGCCATTGCAACCATGATTGATGCTACTGTTGGTATGTTTGCGGTT
ATAGTTGGAGAATTGTCATGACTGACAATCTCAATATTAATTTTAAAAGGTCAATCCCCCTTTGTTCTGTTGTTGTGATA
AATAGCTAACCTGATAAAGTTGAAGGAAGGAAATTGTTTATTTTCTGTGATGTTCAAAGCATGGATGAGAAGACCCTATA
CTCAGAGGCAACAAGC

Alignment

ORF - retro_amel_1301 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 66.5 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 6
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  RSFASEVIRVDLSLP-NPSWSKDMRLLFDQFMKKTEDGSWKRLPSYKYVSP-QRTEVKTFFP-DGKPVKE
          R.F.SE.I....SLP..PSW.KDMRL..DQFMKK.EDG..KRLPSY...S.......KTFF..D.KPV..
Retrocopy R*FSSEIINRNRSLP<MPSWGKDMRLFIDQFMKKCEDGF*KRLPSYECKST*SIKDFKTFFV<DAKPV-Q

Parental  DHMPQAQLFPRSLEEGLGFEYAMFHNHVENRTVCIFQGGPYLQGASGFLHGGAIATMMDSTLGVCALTAG
          ..M..AQLFPRSL.EGLG.EY..FHNHVE.R.VCIFQGGPYLQGA.GFLHG.AIATM.D.T.G..A...G
Retrocopy *QMS*AQLFPRSLKEGLGLEYVIFHNHVEERIVCIFQGGPYLQGAPGFLHGAAIATMIDATVGMFAVIVG

Parental  -GVAMTANLNINFRRPIPLCSVVVINSQLDKVEGRKLFVSCNVQSVDGKTLHSKATS
          ....MT.NLNINF.R.IPLCSVVVINS..DKVEGRKLF..C.VQS.D.KTL.S.ATS
Retrocopy <RIVMTDNLNINFKRSIPLCSVVVINS*PDKVEGRKLFIFCDVQSMDEKTLYSEATS

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_1301 retrocopy.

TSS

Ailuropoda melanoleuca was not studied using FANTOM5 data.

Lab

retro_amel_1301 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 20 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000000355	1 retrocopy	retro_amel_1301 ,
Choloepus hoffmanni	ENSCHOG00000000818	1 retrocopy	retro_chof_841,
Dasypus novemcinctus	ENSDNOG00000005970	1 retrocopy	retro_dnov_710,
Felis catus	ENSFCAG00000003443	1 retrocopy	retro_fcat_387,
Homo sapiens	ENSG00000159445	2 retrocopies	retro_hsap_1569, retro_hsap_978,
Gorilla gorilla	ENSGGOG00000008114	2 retrocopies	retro_ggor_1195, retro_ggor_782,
Microcebus murinus	ENSMICG00000010696	4 retrocopies	retro_mmur_1241, retro_mmur_1436, retro_mmur_1505, retro_mmur_1574,
Nomascus leucogenys	ENSNLEG00000010322	1 retrocopy	retro_nleu_1737,
Oryctolagus cuniculus	ENSOCUG00000005194	1 retrocopy	retro_ocun_1341,
Pongo abelii	ENSPPYG00000000851	1 retrocopy	retro_pabe_1295,
Pan troglodytes	ENSPTRG00000001301	2 retrocopies	retro_ptro_1056, retro_ptro_768,
Tupaia belangeri	ENSTBEG00000003352	2 retrocopies	retro_tbel_2412, retro_tbel_3266,
Tarsius syrichta	ENSTSYG00000005739	1 retrocopy	retro_tsyr_579,