RetrogeneDB ID: retro_amel_1242

Retrocopy location

• Organism: Panda (Ailuropoda melanoleuca)
• Coordinates: GL193085.1:606464..607751(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSAMEG00000016652
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: MRPS5
• Ensembl ID: ENSAMEG00000009757
• Aliases: None
• Description: mitochondrial ribosomal protein S5 [Source:HGNC Symbol;Acc:14498]

Sequence

>retro_amel_1242
GCGGTCGCGGTGCGCGCTGCGGGCTGCCTCCCTGTGCTGTGTGGCGCGCGCGCGGCGGGGGGGCGGGGGGGGTGGTCACA
GCTTTACCTAAACACCTTTCCAACAGCTTCCATTTCGGCATTGAAGACTGTTCTCAGCAACAACCCTTTGTCATATCCAG
GAATCAGAGACAACCATCATTTCACCAGCTTGCCCCGTGGCTACAGACACAATGCTGTATTTCTTCTCCCAGTAATTTAA
TGGGTCAACAGTATAAATCCTATAATTTCTTCATTAAATTGACAGCAGATGAGCTTTGGAAAGGTGCTTTGGCAGAGACT
GGAGCAGGAGCAAGAAAAGGAAATGGGAAAAGAACTAAGAAAAAGAGAACAAAGGATCTGAACAAGGCTCAGATCATTGG
TGAAAGGTGTCACGGCTTCCTCTGGCCTGGTCTGAATGTCCCTCTTATGAGAGAGGGAGCTGTGCAGACCGTTGCCCAAA
GAAGCAAGGAAGAGCAGGAGAAGGTAGAGGCTGACCTGGTCCAGCAGAGGGAAGAGTGGGACCGCAAGAGGAAGAGGAAG
GTTAAACGGGAGCGAGGATGGAGCAGAAACATATGGGGAGGCGTCAGTCTTGGCCCCCCTGACCATGGTCCCAAAGGAGA
AACATATGATGATTTTGATGCCAGGATACTTGAAGTAAGAAATGTTTTCAATATGACAGCAAAAGAGGGAGGAAAAGAAA
CCAGCCCGAGTCCTGGTTGGTGTGGGGAACGGCAGAGGAGCTACAGGTTTTGCCACTGGGAAAGACATTGATCAGGTGGA
CGCTTTCAGAAAAGCAAAGAACAGAGCAGTTTGCTATTTGCATTATATAGAACGATGAGAAGACCATATGATATTCCGTG
ATATTTCTTTAAGATTTAAAAGGACCCATATCAAGATAAAGAAACAACCCAGGGGCTACGGCCTCCACAGCCATGGGGCC
ATCGTCACCATCTGCCAGCTCATTGGCATCAAAGACATGTCTGCCAAGGTCTCTGGGTTGGTCCACATGGTCAACCTCCC
ACGGGGTCTTTTCCATGGGCTCTCACACAAGGAAACCCATCAACAACTGGCTAAGAGTCTCCACTTGGTAGAATTCCGGG
AGGAATATGGCCCTCTGCCCATCGTGGTGGCCTCCCACCAGGAAGCCTTGAGAAAGGATCCAAAGCCAGAAGATGAGGTT
CCAGACATCAAACTGGACTGGGAAGAAGTGAAGGCCGCACAGGGAATGAAGCACTTAGTGTGGTCGAGTTTAAAGAGAGC
CGCCACC

Alignment

ORF - retro_amel_1242 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 80.65 %
• Parental protein coverage: 99.77 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  AVAVRAAGYLPALCGVPAGHV---WSRQLYRNTFPTASILALKTVRSNGPSSSLGTRDNHHFTSLTHA-L
          AVAVRAAG.LP.LCG..A......WS.QLY.NTFPTASI.ALKTV.SN.P.S..G.RDNHHFTSL....L
Retrocopy AVAVRAAGCLPVLCGARAXXXXXXWS-QLYLNTFPTASISALKTVLSNNPLSYPGIRDNHHFTSLPRG<L

Parental  QTQCCISSPSNSMGQQYRSYSFFTKLTADELWKGALAETGAGARKGRGKRTKKKRKKDLNRGQIIGEGRR
          QTQCCISSPSN.MGQQY.SY.FF.KLTADELWKGALAETGAGARKG.GKRTKKKR.KDLN..QIIGE...
Retrocopy QTQCCISSPSNLMGQQYKSYNFFIKLTADELWKGALAETGAGARKGNGKRTKKKRTKDLNKAQIIGERCH

Parental  GFLWPGLNVPLMREGAVQTIAQRSKEDQEKVEADLVQQREEWDRKRKRKVKRERGWSGNTWGGVSLGPPD
          GFLWPGLNVPLMREGAVQT.AQRSKE.QEKVEADLVQQREEWDRKRKRKVKRERGWS.N.WGGVSLGPPD
Retrocopy GFLWPGLNVPLMREGAVQTVAQRSKEEQEKVEADLVQQREEWDRKRKRKVKRERGWSRNIWGGVSLGPPD

Parental  PGPSGETYDDFDTRVLEVRNVFNMTAKEG-RKKSVRVLVAVGNGRGAAGFAVGKAADRMDAFRKAKNRAV
          .GP.GETYDDFD.R.LEVRNVFNMTAKEG..KK..RVLV.VGNGRGA.GFA.GK..D..DAFRKAKNRAV
Retrocopy HGPKGETYDDFDARILEVRNVFNMTAKEG>EKKPARVLVGVGNGRGATGFATGKDIDQVDAFRKAKNRAV

Parental  HYLHYIERYEDHTIFHDISLRFKKTHIKMKKQPRGYGLRCHRAIITICRLIGIKDMYAKVSGSLNMLNLT
          .YLHYIER.EDH.IF.DISLRFK.THIK.KKQPRGYGL..H.AI.TIC.LIGIKDM.AKVSG...M.NL.
Retrocopy CYLHYIER*EDHMIFRDISLRFKRTHIKIKKQPRGYGLHSHGAIVTICQLIGIKDMSAKVSGLVHMVNLP

Parental  RGLFHGLSRQETHQQLADKKSLHVIEFREECGPLPIVVASPQGALRKDPEPEDEVPDIKLDWEEVRAAQG
          RGLFHGLS..ETHQQLA..KSLH..EFREE.GPLPIVVAS.Q.ALRKDP.PEDEVPDIKLDWEEV.AAQG
Retrocopy RGLFHGLSHKETHQQLA--KSLHLVEFREEYGPLPIVVASHQEALRKDPKPEDEVPDIKLDWEEVKAAQG

Parental  MKRSVWSNLKRAAT
          MK..VWS.LKRAAT
Retrocopy MKHLVWSSLKRAAT

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_1242 retrocopy.

TSS

Ailuropoda melanoleuca was not studied using FANTOM5 data.

Lab

retro_amel_1242 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 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000009757	1 retrocopy	retro_amel_1242 ,
Gorilla gorilla	ENSGGOG00000001750	1 retrocopy	retro_ggor_2139,
Myotis lucifugus	ENSMLUG00000003183	1 retrocopy	retro_mluc_2245,
Macaca mulatta	ENSMMUG00000016239	2 retrocopies	retro_mmul_2110, retro_mmul_2251,
Mus musculus	ENSMUSG00000027374	1 retrocopy	retro_mmus_2014,