RetrogeneDB ID: retro_amel_1395

Retrocopy location

• Organism: Panda (Ailuropoda melanoleuca)
• Coordinates: GL193317.1:528004..528411(-)
• Located in intron of: None

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_1395
ATACTGGAAGTAGATGTGTTGAAGCAGAATACTGATTTGTCCACAGGCTTCATATCCACTGATTCCTCGTGATGGAGTGG
GGGTTGCACACTCTTGCAAAAGTGTTGAACCTTCAGATTTTAGGAACTAGTGGATCTTTGATATATATCAAAGAACATTC
TGTTGTGGATCCAGTGGTAAAGAAAATGGAATTTTGTGCCGCTTACATCACATTCACAAATTTAATGTCAGTTAATGCAA
GGTTGGTAGATGCTCCTCGTCCAGAGAATCCTGGAATGACCGTGCTGATGCAAGAAGCTATCGCCACTGTGAAAGGAATT
AGCCGAGGGAGGCATATGGGAAGTTTAAAGACAAACACTATGTCATCTGATCCAAAGAATGGTCAAGGTGCCTTGGAAGC
GGTGATC

Alignment

ORF - retro_amel_1395 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 55.47 %
• Parental protein coverage: 75.86 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  VVGVDVLERSVDSRG-RLHSHRLLSTEWGLPGFVKA----ILGTSRTLTYIKEHSVVDPVEKKMELCSTN
          ...VDVL....D....RLH.H..L..EWGL....K.....ILGTS..L.YIKEHSVVDPV.KKME.C...
Retrocopy ILEVDVLKQNTDLST<RLHIH*FLVMEWGLHTLAKVLNLQILGTSGSLIYIKEHSVVDPVVKKMEFCAAY

Parental  ITLTNLVSVNERLVYTPHPEDPELTVLTQEAIITVKGISLGSYLESLMANTISSNARKGWAAIEWII
          IT.TNL.SVN.RLV..P.PE.P..TVL.QEAI.TVKGIS.G....SL..NT.SS....G..A.E..I
Retrocopy ITFTNLMSVNARLVDAPRPENPGMTVLMQEAIATVKGISRGRHMGSLKTNTMSSDPKNGQGALEAVI

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_1395 retrocopy.

TSS

Ailuropoda melanoleuca was not studied using FANTOM5 data.

Lab

retro_amel_1395 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 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,