RetrogeneDB ID: retro_amel_1399

Retrocopy location

• Organism: Panda (Ailuropoda melanoleuca)
• Coordinates: GL193327.1:620559..620900(-)
• Located in intron of: ENSAMEG00000018426

Retrocopy information

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

Parental gene information

• Parental gene symbol: HDDC2
• Ensembl ID: ENSAMEG00000009635
• Aliases: None
• Description: HD domain containing 2 [Source:HGNC Symbol;Acc:21078]

Sequence

>retro_amel_1399
GTTCCCAAAGAAGAGCATCTTAACAAAGACCAGAAGCTAAGAAGCAAGCAAGTAACCTAGCTCCTCACAGAGGATCTCAG
AAAGGAACTTTACAAACTTTGGGGAAAGTATGAGACCCAATCCTGTGCAGAGGCCAAATTTGTGAACCAGGTAAACCAAT
GTGAGATGATTCTTCAGGCATGTGATTATGAAGACCTTGAAAACAAACCTGGGAGGCTGCAGGACTTCTATAATTCCACA
GCAGGAAAATTCAGTCACCCTGAGATAGTTCAACTTGTTTCTGAACTTGAAGGGGAAAGAAAACACTAACATAGCTGCCA
CGACCAAGTGAGCCACCCTCC

Alignment

ORF - retro_amel_1399 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 71.3 %
• Parental protein coverage: 54.9 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  IPKEEKHRREEEAM-KQLTQLLPEDLRKELYELWEEYETQSSAEAKFVKQLDQCEMILQASEYEDLENRP
          .PKEE..........KQ.T.LL.EDLRKELY.LW..YETQS.AEAKFV.Q..QCEMILQA..YEDLEN.P
Retrocopy VPKEEHLNKDQKLRSKQVT*LLTEDLRKELYKLWGKYETQSCAEAKFVNQVNQCEMILQACDYEDLENKP

Parental  GRLQDFYDSTAGKFSHPEIVQLVSELEAER-NASIAAA-PREPSS
          GRLQDFY.STAGKFSHPEIVQLVSELE.ER.N..IAA..P.EP.S
Retrocopy GRLQDFYNSTAGKFSHPEIVQLVSELEGER>NTNIAAT>PSEPPS

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_1399 retrocopy.

TSS

Ailuropoda melanoleuca was not studied using FANTOM5 data.

Lab

retro_amel_1399 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 5 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000009635	1 retrocopy	retro_amel_1399 ,
Canis familiaris	ENSCAFG00000001030	1 retrocopy	retro_cfam_2179,
Microcebus murinus	ENSMICG00000014059	1 retrocopy	retro_mmur_549,
Tupaia belangeri	ENSTBEG00000011826	1 retrocopy	retro_tbel_4277,
Tursiops truncatus	ENSTTRG00000002258	1 retrocopy	retro_ttru_1086,