RetrogeneDB ID: retro_amel_361

Retrocopy location

• Organism: Panda (Ailuropoda melanoleuca)
• Coordinates: GL192402.1:1004999..1005871(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSAMEG00000010846
• Aliases: None
• Description: Malate dehydrogenase [Source:UniProtKB/TrEMBL;Acc:G1LWG5]

Sequence

>retro_amel_361
AGCCCCTTAGTGAGCCGTCTGACCCTGTACGATATTGCTCAGACACTCCGAGTGGCCTCAGATCTGAACCACATGGAGAC
CAGAGCAACCATGAAAGCCTGCCTCACACCCACGCAGGTGCCACTCTGCATGAGAGGTTGCGATGTGGTGGTTTTTCCAG
CAGGAGTCCTGAGGAAACCAGGCAGCACAGGGATGACCTGTTCAACACCAGTGCCCTGATTGTGGCCACCCTGGCTGCCG
CTTGCACCCGGCATTGCCCTGAGGCCATGATCTGCATCATTTCAAATCTGGTTAACTCCATCATCCCAATGGTAATGGAA
GTTTTCAAGAAACATGGAGCATACCACCCCAATAAAATCTTTGGGGTGACCACTCTGGATGTTGTCAGAGCCAACACTTT
TATTGCAGGACTGAGGGGTTTGGATCCTGCTTGAGTTGATGTTCCTATCCCCAGGGGCCATGCAGGGAAGACCATCACCC
CCTGATCTCCCAGGGCACTCCCAAGGTGGACGTTCCCTGGGACCAGCTGACAGCCGTCACTGGGAAGATCCAGGAGGCCC
TCATGGAGGTGGTGACGGTCAAAGCTAGAGCAGGCTCTGCCACCCTGTCCATGGCTATGCGGGAGCCTGGTTTGTCTTCT
CCCTTGTGGAGGCAAGGAACGGAAAGGAAGGAGTTGTCCAATGTTCCTTCGTTAAGTCTCAAGAAAAAGATGGTGCCTGT
TTCTCCACACCATTATTGCTGGGGGCCAAGGGCATCTAGAAGAATCCAGGCATCGACAAATCTCCCCTTTCAAAGAGAAG
ATGATAGCAGAAGCCATCCCTGAGCTGAAGGCCTCCATCAAGGAGGGAGAGGAGTCTGTGAAGAAGATGAAA

Alignment

ORF - retro_amel_361 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 77.03 %
• Parental protein coverage: 86.39 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  SPLVSRLTLYDIAHTPGVAADLSHIETRATVKGYLGPEQLPDCLKGCDVVVIPAGVPRKPGMT-RDDLFN
          SPLVSRLTLYDIA.T..VA.DL.H.ETRAT.K..L.P.Q.P.C..GCDVVV.PAGV.RKPG.T.RDDLFN
Retrocopy SPLVSRLTLYDIAQTLRVASDLNHMETRATMKACLTPTQVPLCMRGCDVVVFPAGVLRKPGST<RDDLFN

Parental  TNASIVATLTAACAQHCPEAMICVISNPVNSTIPIATEVFKKHGAYNPNKIFGVTTLDIVRANTFIAELK
          T.A.IVATL.AAC..HCPEAMIC.ISN.VNS.IP...EVFKKHGAY.PNKIFGVTTLD.VRANTFIA.L.
Retrocopy TSALIVATLAAACTRHCPEAMICIISNLVNSIIPMVMEVFKKHGAYHPNKIFGVTTLDVVRANTFIAGLR

Parental  GLDPARVNVPVIGGHAGKTII-PLISQCAPKVDLPQDQLTAVTGRIQEAGTEVVKAKAGAGSATLSMA-Y
          GLDPA.V.VP...GHAGKTI..PLISQ..PKVD.P.DQLTAVTG.IQEA..EVV..KA.AGSATLSMA.Y
Retrocopy GLDPA*VDVPIPRGHAGKTIT<PLISQGTPKVDVPWDQLTAVTGKIQEALMEVVTVKARAGSATLSMA<Y

Parental  AGARFVFSLVDAMNGKEGVVECSFVKSQEADCAYFSTPLLLGKKGIEKNLGIGK-ISPFEEKMIAEAIPE
          AGA.FVFSLV.A.NGKEGVV.CSFVKSQE.D.A.FSTPLLLG.KGI.KN.GI.K.ISPF.EKMIAEAIPE
Retrocopy AGAWFVFSLVEARNGKEGVVQCSFVKSQEKDGACFSTPLLLGAKGI*KNPGIDK<ISPFKEKMIAEAIPE

Parental  LKASIKKGEEFVKNMK
          LKASIK.GEE.VK.MK
Retrocopy LKASIKEGEESVKKMK

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_361 retrocopy.

TSS

Ailuropoda melanoleuca was not studied using FANTOM5 data.

Lab

retro_amel_361 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 14 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000010846	1 retrocopy	retro_amel_361 ,
Canis familiaris	ENSCAFG00000013515	2 retrocopies	retro_cfam_182, retro_cfam_41,
Myotis lucifugus	ENSMLUG00000017795	1 retrocopy	retro_mluc_1948,
Monodelphis domestica	ENSMODG00000013680	1 retrocopy	retro_mdom_1711,
Mustela putorius furo	ENSMPUG00000016000	2 retrocopies	retro_mputfur_1607, retro_mputfur_478,
Mus musculus	ENSMUSG00000019179	1 retrocopy	retro_mmus_2451,
Otolemur garnettii	ENSOGAG00000009705	1 retrocopy	retro_ogar_3068,
Pteropus vampyrus	ENSPVAG00000003397	1 retrocopy	retro_pvam_981,
Tupaia belangeri	ENSTBEG00000003190	1 retrocopy	retro_tbel_440,
Tursiops truncatus	ENSTTRG00000014834	1 retrocopy	retro_ttru_1550,
Drosophila melanogaster	FBgn0262559	2 retrocopies	retro_dmel_54, retro_dmel_76,