RetrogeneDB ID: retro_amel_1162

Retrocopy location

• Organism: Panda (Ailuropoda melanoleuca)
• Coordinates: GL192980.1:582828..583693(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSAMEG00000006872
• Aliases: None
• Description: None

Sequence

>retro_amel_1162
AGCATGAGTGAATGCATCTCTATCCACGGTGGCCAGGCTGGGGTCCAGACTGGCAATGCTTGCTGGGAGCTCTACTGCCT
GGAACATGGCATCCAGCCCGATGGTCAGATGCCAAGTGACAGGACCACTGGGGGAGGAGATGACTCCTTCGACACCTTCT
TCAGGGAGATGGGCACTGGCCCGCATGTGCCCAGGGCAGTGTTTGTAAACCTGGAACCCGTGGTCATTGATGAAGTTCAC
CCTGGCACCTGCTGCCAGCTTGTCCACCCTGAGCAGCTCATCACAGGCAAGGAAGATGTCCCCAATATGCCCAAGGGAAC
AGTGCACCATCGGCAAGGAGATCACTGACCATGACTTGGACCGAATTCAGAAACTGGCTGACCAATGCACAGTCTTCCGG
GCTTCTTGGTTTCCACAGCTTTGGAGGAGGAACTAGTTCCATCACCTCCCGCTGATGGAAAGTCTGTCGATCATGGCAAG
AAGTCCAAGCTGGAGTTCTCCATTTACCCAGCCCCCCAGGTTTCCAGCTGTAGTTGAGCCCCACAACTCCATCCTCACCA
CCGACAGCACCCTGGAGCACTCAGATTGTGCCTTCGTGGTAGACAACGAGGCCATCAATGAGTTCTGTCGCAGAAATCTC
GATATTGAACTCCCAACCTACGCTAACCTGAATAGGGTGATAGGTCAGATTGTGTCCTCCATCACCGCTTCCCTCGGATT
TGATGGAGCCCTGAATGTTGATCTGACAGAGTTCCAGACCAACCTGGAGCCCTATCCCCACATCCACTTCCCTCTGGCCA
CCTATGCCCCTGTCCTCTCTGCTGAGAAAGCCTGCCACGAACAGCTTTCTGTAGCAGAGATCACC

Alignment

ORF - retro_amel_1162 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 74.41 %
• Parental protein coverage: 64.54 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  SKRECISIHVGQAGVQIGNACWELYCLEHGIQPDGQMPSDKTIGGGDDSFNTFFSETGAGKHVPRAVFVD
          S..ECISIH.GQAGVQ.GNACWELYCLEHGIQPDGQMPSD.T.GGGDDSF.TFF.E.G.G.HVPRAVFV.
Retrocopy SMSECISIHGGQAGVQTGNACWELYCLEHGIQPDGQMPSDRTTGGGDDSFDTFFREMGTGPHVPRAVFVN

Parental  LEPTVIDEVRTGTYRQLFHPEQLITGKEDAANNYARG-HYTIGKEIIDLVLDRIRKLADQCT-GLQGFLV
          LEP.VIDEV..GT..QL.HPEQLITGKED...N...G...TIGKEI.D..LDRI.KLADQCT..L.GFLV
Retrocopy LEPVVIDEVHPGTCCQLVHPEQLITGKEDVP-NMPKG>QCTIGKEITDHDLDRIQKLADQCT<SLPGFLV

Parental  -FHSFGGGTGSGFTSL-LMERLSVDYGKKSKLEFSIYPAPQVSTAVVEPYNSILTTHTTLEHSDCAFMVD
          .FHSFGGGT.S..TS..LME..S......S....S....P....AVVEP.NSILTT..TLEHSDCAF.VD
Retrocopy <FHSFGGGT-SSITSR<LME--SLSIMARSPSWSSPFTQPPRFPAVVEPHNSILTTDSTLEHSDCAFVVD

Parental  NEAIYDICRRNLDIERPTYTNLNRLISQIVSSITASLRFDGALNVDLTEFQTNLVPYPCIHFPLATYAPV
          NEAI...CRRNLDIE.PTY.NLNR.I.QIVSSITASL.FDGALNVDLTEFQTNL.PYP.IHFPLATYAPV
Retrocopy NEAINEFCRRNLDIELPTYANLNRVIGQIVSSITASLGFDGALNVDLTEFQTNLEPYPHIHFPLATYAPV

Parental  ISAEKAYHEQLSVAEIT
          .SAEKA.HEQLSVAEIT
Retrocopy LSAEKACHEQLSVAEIT

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_1162 retrocopy.

TSS

Ailuropoda melanoleuca was not studied using FANTOM5 data.

Lab

retro_amel_1162 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 14 parental genes, and 39 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000006872	4 retrocopies	retro_amel_1162 , retro_amel_1367, retro_amel_1387, retro_amel_1895,
Ailuropoda melanoleuca	ENSAMEG00000011042	2 retrocopies	retro_amel_488, retro_amel_518,
Canis familiaris	ENSCAFG00000008640	8 retrocopies	retro_cfam_1481, retro_cfam_1751, retro_cfam_1895, retro_cfam_1917, retro_cfam_1979, retro_cfam_2000, retro_cfam_463, retro_cfam_926,
Choloepus hoffmanni	ENSCHOG00000008444	2 retrocopies	retro_chof_179, retro_chof_360,
Cavia porcellus	ENSCPOG00000013016	1 retrocopy	retro_cpor_96,
Felis catus	ENSFCAG00000027011	1 retrocopy	retro_fcat_588,
Felis catus	ENSFCAG00000028689	3 retrocopies	retro_fcat_1802, retro_fcat_254, retro_fcat_798,
Loxodonta africana	ENSLAFG00000010021	1 retrocopy	retro_lafr_326,
Microcebus murinus	ENSMICG00000017551	3 retrocopies	retro_mmur_144, retro_mmur_705, retro_mmur_885,
Myotis lucifugus	ENSMLUG00000002622	4 retrocopies	retro_mluc_154, retro_mluc_186, retro_mluc_234, retro_mluc_270,
Otolemur garnettii	ENSOGAG00000009435	1 retrocopy	retro_ogar_240,
Tupaia belangeri	ENSTBEG00000001671	1 retrocopy	retro_tbel_3700,
Tarsius syrichta	ENSTSYG00000013266	7 retrocopies	retro_tsyr_1014, retro_tsyr_1278, retro_tsyr_1281, retro_tsyr_1679, retro_tsyr_1834, retro_tsyr_243, retro_tsyr_6,
Tursiops truncatus	ENSTTRG00000004794	1 retrocopy	retro_ttru_407,