RetrogeneDB ID: retro_amel_1448

Retrocopy location

• Organism: Panda (Ailuropoda melanoleuca)
• Coordinates: GL193391.1:288763..289464(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: DRG1
• Ensembl ID: ENSAMEG00000007040
• Aliases: None
• Description: developmentally regulated GTP binding protein 1 [Source:HGNC Symbol;Acc:3029]

Sequence

>retro_amel_1448
AAGGAAGTCATTGCAGTGGCCTGAGCATGTAATTTGATCCTTGTTGTTCTGGATGTCCCGGAATCATTGGGACCTGAGAA
GAGAATTGAAAACAAGCTGGAAGCCTTTAGCATTTACTTGAACAGCAAACCCCCTAACATTGGCTTTAAGAAGAAGGATG
AGAGAGGCATCAATCTCACTGTCACTTGCCCTCAAAGTGAACTGGAAGCTGAGAGTGTGAAGAGCATTCTGGCTAAATAT
AAAATTAGTAATGCTGGTGTGGCTCTGCATAGTGATGTCACAGCAGATGACTTCATTGACAGTGGTGGAAGGAAACAGAG
TCTATATCCTTTGTATCGACGTGTTAAATAAGATTGAGCAGATCTCCACTGAAGAACTGGATATCATCTATAAGGTGCCT
CACTATGCATTCTTCTCTGTCCATTACTGCTGGAATTTTGGTGAACTGTTGGAAAATATCTGCTACTAACAAACACTAGT
GAGGATTTCACCAAACACAAAGGCCAGTTGCCAGATTACATACCTCCAAGGGTGCTGCCTAAACCCAGGATCACATGGAG
GATTTCCACATGAATATTCACAAAAACCTTATCAAAGAATTAAATATCTTTCAGTCTGGGGGACCCTCTGTGAAACACAA
TTCTCAGAAAGTGGGTTGAGTCCATATATTAGAGAATGAGAACATCATTCATTGTGAAAAA

Alignment

ORF - retro_amel_1448 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 68.2 %
• Parental protein coverage: 63.76 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  RQVIAVARTCNLILIVLDVLKPLGHKKIIENELEGFGIRLNSKPPNIGFKKKDKGGINLTATCPQSELDA
          ..VIAVA..CNLIL.VLDV...LG..K.IEN.LE.F.I.LNSKPPNIGFKKKD..GINLT.TCPQSEL.A
Retrocopy KEVIAVA*ACNLILVVLDVPESLGPEKRIENKLEAFSIYLNSKPPNIGFKKKDERGINLTVTCPQSELEA

Parental  ETVKSILAEYKIHNADVTLRSDATADDLID-VVEGNRVYIPCIYVLNKIDQISIEELDIIYKVPHCVPIS
          E.VKSILA.YKI.NA.V.L.SD.TADD.ID.VVEGNRVYI.CI.VLNKI.QIS.EELDIIYKVPH....S
Retrocopy ESVKSILAKYKISNAGVALHSDVTADDFID>VVEGNRVYILCIDVLNKIEQISTEELDIIYKVPHYAFFS

Parental  AHHRWNFDDLLEKIWDYLKLVRI-YTKPKGQLPDYTSPVVLPYSRTT-VEDFCMKIHKNLIKE-FKYALV
          .H..WNF..LLE.I.....LVRI..TK.KGQLPDY..P.VLP..R.T..EDF.M.IHKNLIKE..KY..V
Retrocopy VHYCWNFGELLENICY*QTLVRI<FTKHKGQLPDYIPPRVLPKPRIT<MEDFHMNIHKNLIKE<IKYLSV

Parental  WGL-SVKHNPQKVGKDHTLEDEDVIQIVK
          WG..SVKHN.QKVG..H.LE.E..I...K
Retrocopy WGT>SVKHNSQKVG*VHILENENIIHCEK

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_1448 retrocopy.

TSS

Ailuropoda melanoleuca was not studied using FANTOM5 data.

Lab

retro_amel_1448 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 17 parental genes, and 27 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000007040	1 retrocopy	retro_amel_1448 ,
Canis familiaris	ENSCAFG00000032601	6 retrocopies	retro_cfam_1535, retro_cfam_1807, retro_cfam_382, retro_cfam_415, retro_cfam_453, retro_cfam_607,
Ciona intestinalis	ENSCING00000003305	1 retrocopy	retro_cint_1,
Callithrix jacchus	ENSCJAG00000011009	4 retrocopies	retro_cjac_1104, retro_cjac_2246, retro_cjac_2606, retro_cjac_855,
Cavia porcellus	ENSCPOG00000010791	1 retrocopy	retro_cpor_1401,
Ciona savignyi	ENSCSAVG00000006503	1 retrocopy	retro_csav_10,
Dasypus novemcinctus	ENSDNOG00000001312	1 retrocopy	retro_dnov_531,
Homo sapiens	ENSG00000185721	1 retrocopy	retro_hsap_2231,
Gorilla gorilla	ENSGGOG00000011185	1 retrocopy	retro_ggor_1665,
Myotis lucifugus	ENSMLUG00000007033	1 retrocopy	retro_mluc_1447,
Macaca mulatta	ENSMMUG00000019099	1 retrocopy	retro_mmul_999,
Mustela putorius furo	ENSMPUG00000012810	1 retrocopy	retro_mputfur_339,
Mus musculus	ENSMUSG00000020457	1 retrocopy	retro_mmus_2366,
Nomascus leucogenys	ENSNLEG00000027001	1 retrocopy	retro_nleu_2627,
Pan troglodytes	ENSPTRG00000014272	1 retrocopy	retro_ptro_1578,
Ictidomys tridecemlineatus	ENSSTOG00000014187	1 retrocopy	retro_itri_460,
Tarsius syrichta	ENSTSYG00000010160	3 retrocopies	retro_tsyr_1374, retro_tsyr_1918, retro_tsyr_405,