RetrogeneDB ID: retro_amel_1698

Retrocopy location

• Organism: Panda (Ailuropoda melanoleuca)
• Coordinates: GL193996.1:87948..88413(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SAR1A
• Ensembl ID: ENSAMEG00000017868
• Aliases: None
• Description: SAR1 homolog A (S. cerevisiae) [Source:HGNC Symbol;Acc:10534]

Sequence

>retro_amel_1698
CATACTCAGTGGTCTGACTGATTGGGCCAACACGTTTCTACATTAGATCTGACATCAGAAGAGCTGAAAATTGCTAGAAT
GCTTTTACAACTTTGATCTTGGTGGGCATGAGCAAGCACATCGAGTTTGGAAAACTTATCTCCCAGCAATCAATAGGATT
GTCATTCTGGTGGATTGTGCAGGTCATCCTCACCTCATGGAAACCACACTTGGGCTAAATGCTTTAATGACCGAGGAAAC
AATTCCCAATGTGCCAATCCATATCTTGGGTAATAAAAATGACAAAGCAGATGCAATCAGTGAGGAAAAGCTCCATGAGA
TATTTGGGCTTTATGGATTGACCACAGGAAAGGAGAATGTGACCCTGAGGGAGCTGAATGCCTGCCCCAAGGGAGTGTTA
CTTGCAGTGCGCTGGAGAAGCAAGGCTATGACAAAGGCTTCCACTGGCTTTCCCAGTAAATTGAT

Alignment

ORF - retro_amel_1698 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 71.07 %
• Parental protein coverage: 78.79 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  HMLKDDRLGQHVPTLHPTSEELTIAGM-TFTT-FDLGGHEQARRVWKNYLPAINGIVFLVDCADHPRLME
          H....D.LGQHV.TL..TSEEL.IA.M..FTT.FDLGGHEQA.RVWK.YLPAIN.IV.LVDCA.HP.LME
Retrocopy HTQWSD*LGQHVSTLDLTSEELKIARM<AFTT<FDLGGHEQAHRVWKTYLPAINRIVILVDCAGHPHLME

Parental  SKVELNALMTDETISNVPILILGNKIDRTDAISEEKLREIFGLYGQTTGKGNVTLKELNARPMEVFM-CS
          ....LNALMT.ETI.NVPI.ILGNK.D..DAISEEKL.EIFGLYG.TTGK.NVTL.ELNA.P..V...CS
Retrocopy TTLGLNALMTEETIPNVPIHILGNKNDKADAISEEKLHEIFGLYGLTTGKENVTLRELNACPKGVLL<CS

Parental  VLKRQGYGEGFRWLSQYID
          .L..QGY..GF.WLSQ.ID
Retrocopy ALEKQGYDKGFHWLSQ*ID

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_1698 retrocopy.

TSS

Ailuropoda melanoleuca was not studied using FANTOM5 data.

Lab

retro_amel_1698 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 5 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000017849	1 retrocopy	retro_amel_1075,
Ailuropoda melanoleuca	ENSAMEG00000017868	1 retrocopy	retro_amel_1698 ,
Gorilla gorilla	ENSGGOG00000024879	3 retrocopies	retro_ggor_144, retro_ggor_2408, retro_ggor_2929,
Mustela putorius furo	ENSMPUG00000004338	1 retrocopy	retro_mputfur_225,
Oryctolagus cuniculus	ENSOCUG00000004547	1 retrocopy	retro_ocun_638,