RetrogeneDB ID: retro_amel_728

Retrocopy location

• Organism: Panda (Ailuropoda melanoleuca)
• Coordinates: GL192592.1:1846404..1846737(+)
• Located in intron of: ENSAMEG00000006161

Retrocopy information

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

Parental gene information

• Parental gene symbol: AK4
• Ensembl ID: ENSAMEG00000014969
• Aliases: None
• Description: adenylate kinase 4 [Source:HGNC Symbol;Acc:363]

Sequence

>retro_amel_728
AAACTTGAGATAGTGATCACTTAGAACATTCCATTTGAAACATTCAAAGATCGCCTCAGCCGACGTTGGATTCACCCTCC
TAGTGAAAGGGTATATAACCTGGACTTTAATCCACATCATGTACATGGGATTGATGACATCATGGGTGAACCATTAGTCC
AGCAGGATGATAAACCCGAAGCCGAGGCTGCCAGTCTAAGACAGTACAAGGATGTGGCAAAGCCAGTCATTGAATTATAC
AAGAGCCGAGGAGTGCTTCACCAGTTTTCTGTCACAGAGACTAACAAAATCTGGCGCTATGTTTACATGCTTTTCTTGAA
CAAGGTCAAACCA

Alignment

ORF - retro_amel_728 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 83.04 %
• Parental protein coverage: 50.22 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  ELDLVITLNIPFETLKDRLRRRWIHPPSGRVYNLDFNPPHVHGIDDVTGEPLVQQEDDKPEAVAARLRQY
          .L..VIT.NIPFET.KDRL.RRWIHPPS.RVYNLDFNP.HVHGIDD..GEPLVQQ.DDKPEA.AA.LRQY
Retrocopy KLEIVIT*NIPFETFKDRLSRRWIHPPSERVYNLDFNPHHVHGIDDIMGEPLVQQ-DDKPEAEAASLRQY

Parental  KDVAKPVIELYKSRGVLHQFSGTETNKIWPYVYTLFSNKITP
          KDVAKPVIELYKSRGVLHQFS.TETNKIW.YVY.LF.NK..P
Retrocopy KDVAKPVIELYKSRGVLHQFSVTETNKIWRYVYMLFLNKVKP

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_728 retrocopy.

TSS

Ailuropoda melanoleuca was not studied using FANTOM5 data.

Lab

retro_amel_728 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 4 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000002640	3 retrocopies	retro_amel_1009, retro_amel_1916, retro_amel_1931,
Ailuropoda melanoleuca	ENSAMEG00000014969	1 retrocopy	retro_amel_728 ,
Bos taurus	ENSBTAG00000030674	1 retrocopy	retro_btau_782,
Macaca mulatta	ENSMMUG00000001079	3 retrocopies	retro_mmul_104, retro_mmul_1680, retro_mmul_2080,