RetrogeneDB ID: retro_amel_1868

Retrocopy location

• Organism: Panda (Ailuropoda melanoleuca)
• Coordinates: GL194990.1:72033..72870(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RG9MTD2
• Ensembl ID: ENSAMEG00000001076
• Aliases: None
• Description: None

Sequence

>retro_amel_1868
CAAATGAAGAAGCTAATTAAACAGAAACAATGGGAAGAACAACGAGAACTCCGCAAACAAAAGCGGAAGGAAAAACTCAA
AAGAAAACAATTAGAACGACAATGACGTATTCGAAGAGATGTTGTTCACAGCACACTCCGCCTTATCATTGATGGCAGTT
TTGACAGCTCGATGGTATTAAAGGACATTAAGAAGCTTCATAAGCAGATTCAGCGATGCTATGCAGAAAATCGACGAGCA
CTGCATCCTGTGCAGTTTTACTTGACAGGCCATGGAGGCCAGTTGAAAAAGAACATGGATGAAAATGACAAAGGATGGGT
CAACTGGAAGGATATCCACATCAAACCAGAGCATTATAGTGAATTCATAAAGAAAGAAGACCTGATTTACCTAACATCAG
ACTCACCTAATGTACTGAAGGAATGAGATGAATCAAAGGCCTATGTGATTGGAGGCCATCACAAGGGACTCACATAGAAA
CAAGCATCAGATCATGGACTTGGTCATGCACAGCTCCCCCTTGGAAATTTTGTGAAGATGAATAGTAGAAAAGTTTTGGC
AATTAATCATGTGTTTGAGATCATTCTGGAATGTCTGGAAACCAGAGACTGGCAAGAAGCATTTTTTACTATCTTACCCC
AACGGAAAGGAGCTGTTCCCACAGACGAAGCCTGTGAAAGTTCTTCATATGACAAGAAATCTGCCAGGGTTGAAGACGGT
TTGGACAGTGATTCCAGTGAGGAAGAAAATAGCAGAAATGAACCAGAATCACCACATGAAGAAGAAAAACAGGATAAAGA
AAATAGCAATGAGTCTACAGTGAACTCTATACCACAC

Alignment

ORF - retro_amel_1868 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 81.63 %
• Parental protein coverage: 83.98 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  EQRELRKQKRKEKRKRKQLERQCQLESNSDGNDRKRIRRDVVHSTLRLIIDCSFDSLMVLKDIKKLHKQI
          ....L.KQK..E.......................RIRRDVVHSTLRLIID.SFDS.MVLKDIKKLHKQI
Retrocopy QMKKLIKQKQWEEQRELRKQKRKEKLKRKQLERQ*RIRRDVVHSTLRLIIDGSFDSSMVLKDIKKLHKQI

Parental  QRCYAENRRALHPVQFYLTSHGGQLKKNMDENDKGWVNWKDIHIKPEHYSEFIKKEDLIYLTSDSPNVLK
          QRCYAENRRALHPVQFYLT.HGGQLKKNMDENDKGWVNWKDIHIKPEHYSEFIKKEDLIYLTSDSPNVLK
Retrocopy QRCYAENRRALHPVQFYLTGHGGQLKKNMDENDKGWVNWKDIHIKPEHYSEFIKKEDLIYLTSDSPNVLK

Parental  EDESKAYVIGGLVDHNHHKGLTYKQASDHGIGHAQLPLGNFVKMNSRKVLAINHVFEIILEYLETRDWQE
          E.........G.....HHKGLT.KQASDHG.GHAQLPLGNFVKMNSRKVLAINHVFEIILE.LETRDWQE
Retrocopy E*DESKAYVIG----GHHKGLT*KQASDHGLGHAQLPLGNFVKMNSRKVLAINHVFEIILECLETRDWQE

Parental  AFFTILPQRKGAVPTDKACESSSHDKKSARVEDGLDSDSSEEENSRNEPESPHEEEKQDKENSNESTVNS
          AFFTILPQRKGAVPTD.ACESSS.DKKSARVEDGLDSDSSEEENSRNEPESPHEEEKQDKENSNESTVNS
Retrocopy AFFTILPQRKGAVPTDEACESSSYDKKSARVEDGLDSDSSEEENSRNEPESPHEEEKQDKENSNESTVNS

Parental  IPH
          IPH
Retrocopy IPH

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_1868 retrocopy.

TSS

Ailuropoda melanoleuca was not studied using FANTOM5 data.

Lab

retro_amel_1868 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 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000001076	1 retrocopy	retro_amel_1868 ,
Mus musculus	ENSMUSG00000004127	3 retrocopies	retro_mmus_3007, retro_mmus_3008, retro_mmus_3368,
Oryctolagus cuniculus	ENSOCUG00000015213	1 retrocopy	retro_ocun_1482,
Otolemur garnettii	ENSOGAG00000005330	2 retrocopies	retro_ogar_2061, retro_ogar_3335,