RetrogeneDB ID: retro_amel_330

Retrocopy location

• Organism: Panda (Ailuropoda melanoleuca)
• Coordinates: GL192388.1:3183541..3183991(-)
• Located in intron of: ENSAMEG00000001031

Retrocopy information

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

Parental gene information

• Parental gene symbol: SLMO1
• Ensembl ID: ENSAMEG00000012800
• Aliases: None
• Description: slowmo homolog 1 (Drosophila) [Source:HGNC Symbol;Acc:24639]

Sequence

>retro_amel_330
CACCCATCGGAAACTGTTTCGACAGCTGCAATGCAGAAATACCCAAACCCTTTGGACCCAAACGTGGTTGGAAGTGATGT
ACTGGACAGACATATAGATCACTCGGGAAAGCTGCACAGCCAAACACTCCTAAGCACAGAGTGGGGACTGCCTTCCGTTG
TGAAATCTCGTGTTCGTGTAGCAAGAACTAAAACATATGCACAAGATCATTCTGTAGTTGATCCTGCAGAGAAAATGATG
GAACTTAAATCTACTAAAACTTCTCTTCCAATTTGATTGCAGTAGTTAGTATAGAAACCACACCCTCAGGACCCAGAAAA
AACCGTTTTGACACAAGAAGCCATAATCACCGTGAAAGGAGTCAGTCTCAGCAGTTACCTTGAAGGATTGACAGCAACTA
CAATATCTTCAAATGCCAATAAAGGCAGAGAAACAGTGGAATGGGTAATG

Alignment

ORF - retro_amel_330 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 61.44 %
• Parental protein coverage: 87.93 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  HPWDTVIKAAMRKYPNPMNPCVVGVDVLERSVDSRGRLHSHRLLSTEWGLPGFVKAILGTSRTLTYIKEH
          HP..TV..AAM.KYPNP..P.VVG.DVL.R..D..G.LHS..LLSTEWGLP..VK......RT.TY...H
Retrocopy HPSETVSTAAMQKYPNPLDPNVVGSDVLDRHIDHSGKLHSQTLLSTEWGLPSVVKSRVRVARTKTYAQDH

Parental  SVVDPVEKKMELCSTNITLTNLVSVNERLVYTPHPEDPELTVLTQEAIITVKGISLGSYLESLMANTISS
          SVVDP.EK.MEL.ST....T.L......LV..PHP.DPE.TVLTQEAIITVKG.SL.SYLE.L.A.TISS
Retrocopy SVVDPAEKMMELKSTK---TSLPI*LQ*LV*KPHPQDPEKTVLTQEAIITVKGVSLSSYLEGLTATTISS

Parental  NARKGWAAIEWII
          NA.KG....EW..
Retrocopy NANKGRETVEWVM

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_330 retrocopy.

TSS

Ailuropoda melanoleuca was not studied using FANTOM5 data.

Lab

retro_amel_330 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 4 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000012800	2 retrocopies	retro_amel_1395, retro_amel_330 ,
Mus musculus	ENSMUSG00000024530	1 retrocopy	retro_mmus_1332,
Oryctolagus cuniculus	ENSOCUG00000022237	1 retrocopy	retro_ocun_723,
Procavia capensis	ENSPCAG00000001084	1 retrocopy	retro_pcap_66,