RetrogeneDB ID: retro_amel_1745

Retrocopy location

• Organism: Panda (Ailuropoda melanoleuca)
• Coordinates: GL194171.1:222698..223274(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MND1
• Ensembl ID: ENSAMEG00000018446
• Aliases: None
• Description: meiotic nuclear divisions 1 homolog (S. cerevisiae) [Source:HGNC Symbol;Acc:24839]

Sequence

>retro_amel_1745
GGACTGAGTGCAGAGGAACAGAGAGCCCACATGATGGAAATATATTTTGAGTTGAAAGATCTTCAATTAAAGACATGGAG
AAGATTGTCCCCCAAAAGAAAGGCCTTCCTGCTCTGTCAGTAAAAGAAGTCCTTCCAAGTTTAGTTGATGATAGTGTGGT
TGGCTGGGAGAAGATTGGAACATCTAATGATTGTTGGGCTTTTCCAAGGAAAGTTCTTCACGTGAGGAAATGTAGGTAGG
AGGTCTGGAATCTCAGTTATCTGAGAGAAACCAAAAGCACGCAGACCTACCAAAAACCATCCAGAAAATAAAATTGGTTG
ACATGAACCAACCATGCTAGCAAAAGAGCTTTTTAAACTGAGACCAAAGGGAGCAGAAGTAGAAAAATACAAAGAATGTG
ACCTGGAAGTTATAGAGGAAATATGCCAAGCAAATAAAGTAGCCAAAAAAGCTGCTGACAGATGGAGTGATAATGTATTT
GCAATAAAATCTTGGGCCAAAAGAGAAATTGGATTTGAAGAAAATAAAACTGATTTTAAAAATTTTGGGATTCCAGAAGA
CTTAGACTAAATAGAC

Alignment

ORF - retro_amel_1745 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 68.14 %
• Parental protein coverage: 98.04 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  GLSAEEKRARMMEIFFETKDVFQL-KDMEKIAPKEKGITAMSVKEVLQSLVDDGMVDCERIGTSNYYWAF
          GLSAEE.RA.MMEI.FE.KD..QL.KDMEKI.P..KG..A.SVKEVL.SLVDD..V..E.IGTSN..WAF
Retrocopy GLSAEEQRAHMMEIYFELKDL-QL<KDMEKIVPQKKGLPALSVKEVLPSLVDDSVVGWEKIGTSNDCWAF

Parental  PSKALHARKRKLEV-LESQLSEGNQKHASLQKSIEKA-KIGRHETEERTMLAKELSSLRDQREQLKTEVE
          P.K.LH.RK...EV.LESQLSE.NQKHA.L.K.I.K..KIG.HE....TMLAKEL..LR.........VE
Retrocopy PRKVLHVRKCR*EV<LESQLSERNQKHADLPKTIQKI<KIG*HEP---TMLAKELFKLRPKGAE----VE

Parental  KYKECDPQVVEEIRQANKVAKEAANRWTDNIFAIKSWAKRKFGFEENKID-KNFGIPEDFDYID
          KYKECD..V.EEI.QANKVAK.AA.RW.DN.FAIKSWAKR..GFEENK.D.KNFGIPED.D.ID
Retrocopy KYKECDLEVIEEICQANKVAKKAADRWSDNVFAIKSWAKREIGFEENKTDFKNFGIPEDLD*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_1745 retrocopy.

TSS

Ailuropoda melanoleuca was not studied using FANTOM5 data.

Lab

retro_amel_1745 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 11 parental genes, and 17 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000018446	1 retrocopy	retro_amel_1745 ,
Callithrix jacchus	ENSCJAG00000001993	5 retrocopies	retro_cjac_1495, retro_cjac_1907, retro_cjac_2624, retro_cjac_2946, retro_cjac_3979,
Dipodomys ordii	ENSDORG00000004514	1 retrocopy	retro_dord_99,
Felis catus	ENSFCAG00000022084	1 retrocopy	retro_fcat_1833,
Macaca mulatta	ENSMMUG00000004937	1 retrocopy	retro_mmul_395,
Mus musculus	ENSMUSG00000033752	2 retrocopies	retro_mmus_1172, retro_mmus_3281,
Nomascus leucogenys	ENSNLEG00000005936	1 retrocopy	retro_nleu_998,
Oryctolagus cuniculus	ENSOCUG00000004594	2 retrocopies	retro_ocun_1865, retro_ocun_360,
Ochotona princeps	ENSOPRG00000015738	1 retrocopy	retro_opri_1121,
Sorex araneus	ENSSARG00000011001	1 retrocopy	retro_sara_417,
Tupaia belangeri	ENSTBEG00000004475	1 retrocopy	retro_tbel_1734,