RetrogeneDB ID: retro_amel_912

Retrocopy location

• Organism: Panda (Ailuropoda melanoleuca)
• Coordinates: GL192737.1:1086554..1087387(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SNW1
• Ensembl ID: ENSAMEG00000003976
• Aliases: None
• Description: SNW domain containing 1 [Source:HGNC Symbol;Acc:16696]

Sequence

>retro_amel_912
CAGGTGGATGCTGAAGGAAAAATTAAATATGATGCAATTGCTCGGCAAGGTCAGTCAAAAGACAAAGTCATTTATAGCAA
GTACACTGACCTGGTTCCAAAGGAAGTCATGAATGCAGATGACCTGGAACGGCAAAGACCTGATGAAGAAGCCATTAAAG
AGATAACAGAAAAGAAAATGGTAACCCTAGAAAAAACTACATCACAGAAGGTTGCTGCAGCCATGACAGTTCGAGCAGCT
GAAAAACTGGCTCCTGCTCAGTATATTTGACACACACCATCTCAATAAGGAATGGCTTTCAACTCTGGAGCTAAACAGAG
AGTTACTTGGATGGTGGAAATGCAGAAAGATCCAGTGGAACCTCCAAGTTTCAAGATTAATAAGAAAATTCCCCGAGAAC
CACCTTCTCCTCCTACACCTGACATGCATTCTCCTAGCCAAAAGAGGACCGTGAAGGAACAACAAGAGTGGAAGTTTCCT
CCTTGTATTTCAGACTGGAAACATGCAAAGTATTATACAATTCAATTAGACATATGTCTGGCTGCTCATGGAAGAGGGCT
GCAGAGAGTTCACATCAACAAAAACTTTGCCAAGCAGGCTGAAGCCCTCTATATTGCTTATTGGGTGGCTTGTGAAGCTG
TAGAAATATGGGTTCAAGTAGAGAGAAATATGGTTCAAAAAGAAAAGGAGAAACATGAAGAGAAACTTAGAGAAATGCCC
AGAAAGCCAGAGAGAGAAGAGTTGGGATCAAAACCCATGTGGGAAAAGAAGATAGGGAGGCACATGAGAAGGATGAAATC
CAGCATGACAGGTAAAAAGAGAGACAACACAAT

Alignment

ORF - retro_amel_912 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 81.72 %
• Parental protein coverage: 51.87 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  QVDAEGKIKYDAIARQGQSKDKVIYSKYTDLVPKEVMNADDPDRQRPDEEAIKEITEKTRVALEKSVSQK
          QVDAEGKIKYDAIARQGQSKDKVIYSKYTDLVPKEVMNADD..RQRPDEEAIKEITEK..V.LEK..SQK
Retrocopy QVDAEGKIKYDAIARQGQSKDKVIYSKYTDLVPKEVMNADDLERQRPDEEAIKEITEKKMVTLEKTTSQK

Parental  VAAAMPVRAADKLAPAQYIRYTPSQQGVAFNSGAKQRVIRMVEMQKDPMEPPRFKINKKIPRGPPSPPAP
          VAAAM.VRAA.KLAPAQYI..TPSQ.G.AFNSGAKQRV..MVEMQKDP.EPP.FKINKKIPR.PPSPP.P
Retrocopy VAAAMTVRAAEKLAPAQYI*HTPSQ*GMAFNSGAKQRVTWMVEMQKDPVEPPSFKINKKIPREPPSPPTP

Parental  VMHSPSRKMTVKEQQEWKIPPCISNWKNAKGYTIPLDKRLAADGRGLQTVHINENFAKLAEALYIADRKA
          .MHSPS.K.TVKEQQEWK.PPCIS.WK.AK.YTI.LD..LAA.GRGLQ.VHIN.NFAK.AEALYIA...A
Retrocopy DMHSPSQKRTVKEQQEWKFPPCISDWKHAKYYTIQLDICLAAHGRGLQRVHINKNFAKQAEALYIAYWVA

Parental  REAVEMRAQVERKMAQKEKEKHEEKLREM-AQKARERRAGIKTHVEKEDGEARERDEIRHDRRKERQHD
          .EAVE...QVER.M.QKEKEKHEEKLREM.AQKARERR.GIKTHV.KED.EA.E.DEI.HDR.KERQH.
Retrocopy CEAVEIWVQVERNMVQKEKEKHEEKLREM<AQKARERRVGIKTHVGKEDREAHEKDEIQHDR*KERQHN

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_912 retrocopy.

TSS

Ailuropoda melanoleuca was not studied using FANTOM5 data.

Lab

retro_amel_912 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 21 parental genes, and 33 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000003976	2 retrocopies	retro_amel_163, retro_amel_912 ,
Canis familiaris	ENSCAFG00000030409	1 retrocopy	retro_cfam_195,
Callithrix jacchus	ENSCJAG00000016947	2 retrocopies	retro_cjac_2932, retro_cjac_576,
Dipodomys ordii	ENSDORG00000012380	3 retrocopies	retro_dord_693, retro_dord_781, retro_dord_782,
Felis catus	ENSFCAG00000001637	1 retrocopy	retro_fcat_635,
Homo sapiens	ENSG00000100603	1 retrocopy	retro_hsap_174,
Gorilla gorilla	ENSGGOG00000026016	1 retrocopy	retro_ggor_257,
Loxodonta africana	ENSLAFG00000003482	2 retrocopies	retro_lafr_474, retro_lafr_787,
Myotis lucifugus	ENSMLUG00000005228	2 retrocopies	retro_mluc_387, retro_mluc_805,
Monodelphis domestica	ENSMODG00000005252	1 retrocopy	retro_mdom_1841,
Mustela putorius furo	ENSMPUG00000008724	1 retrocopy	retro_mputfur_551,
Mus musculus	ENSMUSG00000021039	2 retrocopies	retro_mmus_1022, retro_mmus_387,
Nomascus leucogenys	ENSNLEG00000016771	1 retrocopy	retro_nleu_982,
Otolemur garnettii	ENSOGAG00000029825	1 retrocopy	retro_ogar_1404,
Ochotona princeps	ENSOPRG00000007568	1 retrocopy	retro_opri_737,
Pongo abelii	ENSPPYG00000006031	1 retrocopy	retro_pabe_454,
Pan troglodytes	ENSPTRG00000006587	1 retrocopy	retro_ptro_165,
Sorex araneus	ENSSARG00000002279	3 retrocopies	retro_sara_403, retro_sara_568, retro_sara_727,
Tupaia belangeri	ENSTBEG00000014074	3 retrocopies	retro_tbel_2575, retro_tbel_2927, retro_tbel_3536,
Taeniopygia guttata	ENSTGUG00000012340	2 retrocopies	retro_tgut_15, retro_tgut_30,
Tarsius syrichta	ENSTSYG00000010951	1 retrocopy	retro_tsyr_1871,