RetrogeneDB ID: retro_amel_1905

Retrocopy location

• Organism: Panda (Ailuropoda melanoleuca)
• Coordinates: GL195482.1:21872..22176(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SNRPD1
• Ensembl ID: ENSAMEG00000002576
• Aliases: None
• Description: small nuclear ribonucleoprotein D1 polypeptide 16kDa [Source:HGNC Symbol;Acc:11158]

Sequence

>retro_amel_1905
ATCAAATTAAAGAATGGAACACAGGTCCATGGAACAATCACAGGTGTGGAGGTCAGCATGAAAACGCATCTTACAGCTAT
GAAAATTACCCCGAAGAATAGAGAAACTATACAACTGGAAATGCTGAATATTCAGGGAAATAACATTTGATATTTTATTT
GCCAGATAGCTTACCTTTGGATACACTACTCATGGATGTTTAACCTAAGATGAGATATAGATAAGGGAAGCTATTGCAGG
AAGAGGCCAAGGCTGAGAAAGAGAAAGAAATCATGGTCAAGGCAGAGAAAGAGGTGGTCCTAGG

Alignment

ORF - retro_amel_1905 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 70.19 %
• Parental protein coverage: 87.18 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  IELKNGTQVHGTITGVDVSMNTHLKAVKMTLKNREPVQLETLSIRGNNIRYFI-LPDSLPLDTLLVDVEP
          I.LKNGTQVHGTITGV.VSM.THL.A.K.T.KNRE..QLE.L.I.GNNI.YFI.LPDSLPLDTLL.DV.P
Retrocopy IKLKNGTQVHGTITGVEVSMKTHLTAMKITPKNRETIQLEMLNIQGNNI*YFI<LPDSLPLDTLLMDV*P

Parental  KVKSK-KREAVAGRGRGRGRGRGRGRGRGRGGPR
          K......REA.AGRG.G..R.R..G.GR.RGGPR
Retrocopy KMRYR<IREAIAGRGQG*ERERNHGQGRERGGPR

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_1905 retrocopy.

TSS

Ailuropoda melanoleuca was not studied using FANTOM5 data.

Lab

retro_amel_1905 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 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000002576	1 retrocopy	retro_amel_1905 ,
Bos taurus	ENSBTAG00000008292	3 retrocopies	retro_btau_144, retro_btau_706, retro_btau_84,
Mustela putorius furo	ENSMPUG00000005567	1 retrocopy	retro_mputfur_185,
Nomascus leucogenys	ENSNLEG00000006822	2 retrocopies	retro_nleu_2824, retro_nleu_945,
Oryctolagus cuniculus	ENSOCUG00000023761	1 retrocopy	retro_ocun_224,
Otolemur garnettii	ENSOGAG00000007833	1 retrocopy	retro_ogar_3085,