RetrogeneDB ID: retro_amel_505

Retrocopy location

• Organism: Panda (Ailuropoda melanoleuca)
• Coordinates: GL192479.1:2440222..2440502(-)
• Located in intron of: ENSAMEG00000010113

Retrocopy information

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

Parental gene information

• Parental gene symbol: MSRB2
• Ensembl ID: ENSAMEG00000006388
• Aliases: None
• Description: methionine sulfoxide reductase B2 [Source:HGNC Symbol;Acc:17061]

Sequence

>retro_amel_505
ACACGGGGGATGCCATTGCTCACCACGAGTGAATGACAAAAGAAACCAACTCCAGAGCAAATTCTGTGTCACGAGAGAGA
AAGGAAGAGAACTGCCTTTCGGTGCGATCAACCCATATAACACGGAGTCAGGCAAGAACGCTGTGTGTGCTGTGGCGGCC
GCTCTTCGGTTTTGAGAGAAAGTACTGCTCTGGAACTGGATGGTTTCTTTCTCTGAGGCTCGTGGGATGTCTGGCTCTGA
TTAAAGTAGCTCAGGGCCCCCTGGACGTGCGGACACCTCA

Alignment

ORF - retro_amel_505 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 56.12 %
• Parental protein coverage: 57.32 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  TKHEPSLTKSEWQKQLTPEQ-FYVTREKGTEPPFSGAYLNNKDSG-MYHCVCCDS-PLFSSEKKYCSGTG
          T...P.LT.SE.QK..TPEQ.F.VTREKG.E.PF......N..SG....CVCC...PLF..E.KYCSGTG
Retrocopy TRGMPLLTTSE*QKKPTPEQ>FCVTREKGRELPFGAINPYNTESG<QERCVCCGG<PLFGFERKYCSGTG

Parental  W-PAFSEAHGTSGSDERDTGILRRVDTS
          W...FSEA.G.SGSD....G...R.DTS
Retrocopy W<VSFSEARGMSGSD*SSSGPPGRADTS

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_505 retrocopy.

TSS

Ailuropoda melanoleuca was not studied using FANTOM5 data.

Lab

retro_amel_505 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.

---

Parental genes homology:

Parental genes homology involve 6 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000006388	1 retrocopy	retro_amel_505 ,
Canis familiaris	ENSCAFG00000004215	1 retrocopy	retro_cfam_1147,
Equus caballus	ENSECAG00000013072	1 retrocopy	retro_ecab_593,
Nomascus leucogenys	ENSNLEG00000012892	1 retrocopy	retro_nleu_2871,
Pongo abelii	ENSPPYG00000002148	1 retrocopy	retro_pabe_3127,
Sus scrofa	ENSSSCG00000011077	1 retrocopy	retro_sscr_218,