RetrogeneDB ID: retro_amel_1890

Retrocopy location

• Organism: Panda (Ailuropoda melanoleuca)
• Coordinates: GL195286.1:8066..8909(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PRKAG2
• Ensembl ID: ENSAMEG00000013406
• Aliases: None
• Description: protein kinase, AMP-activated, gamma 2 non-catalytic subunit [Source:HGNC Symbol;Acc:9386]

Sequence

>retro_amel_1890
GTGTTGTCTCTGATACTACAAGTTAGAAAGGCTTCTGTGCCTTAGCAGCCAATGGCGTTCCAGCAGCACTGTTAAGATAG
AGGACAAAACAATGTTTTGTAGGAATACTAACAATTACAGAGTTCTTAAATACACCACAGACGTGGCATACATCAACCCT
GGTACAGATTTATGAATTAGAGGCACGTAAGATTGAAACAGGGAGGGAGCTTCATCCCCAAGAAACACGTAAGCCTTCAG
GGAATATAGCTCCAGATGCAAAGGTCTTCCATGCTGAAAACTCACTGATCACAAATGAAATCCACTCATTGTCAGTTATT
GATCCTATCAGTAGAGTGCACTTTGTACACGTACCCACAAAGGAATCCTCACCTTCGTGCAGCATTTTAGGTCTGGTCTG
CCAAAGCCTGCCTTCATGAAGCAGAACCTGGATGTTCTTGCATTTGGGCCCACCACAACATCCCTTCATCCTCCAGGAGA
CTCCCATCAGTACAGCCTTGAAAATCTTTGTGGAAAGACAGTTGCTGGCCTTCCTTGTTGTGAATGAGTCAGGAGAAATT
GTGGATATTTACTCCAAGTCTGATTTAATTAAGCTTGCTGTTGAGAAAACGTTCAGTAACCTAGAATCACAGTGACCCAG
GCCCTCAGCACTGCTCACAGTGTCTTGAGGGTGTTGTGATGTACGGTAATCTGGAAATCCTTGACAGATTAGCGTGGGCT
GACCTTGGGCTCCTGGTCGCAAGTGAAGCAGATAGCATCATGGGTGTCATTTCCCTGCCAGATGTGTGGTAAGCCCTGAT
ACTCATGCCCGCAGGTGCCAAACAGAAGGAGACAGAAGCGGAA

Alignment

ORF - retro_amel_1890 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 59.18 %
• Parental protein coverage: 50.62 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 6

Retrocopy - Parental Gene Alignment:

Parental  VFDTTLQVKKA-FFALVANGVRAAPLWESKKQSFVGMLTITDFINILHRYYKSPMVQIYELEEHKIETWR
          V....LQV.KA.F.AL.ANGV.AA.L....KQ.FVG.LTIT.F.N.......S..VQIYELE..KIET.R
Retrocopy VLSLILQVRKA<FCALAANGVPAALLR*RTKQCFVGILTITEFLNTPQTWHTSTLVQIYELEARKIETGR

Parental  ELYLQETFKPLVNISPDASLFDAVYSLIKNKIHRLPVIDPISG-NALYILTHKRILKFLQLFMSDMPKPA
          EL..QET.KP..NI.PDA..F.A..SLI.N.IH.L.VIDPIS...AL...THK.IL.F.Q.F.S..PKPA
Retrocopy ELHPQETRKPSGNIAPDAKVFHAENSLITNEIHSLSVIDPISR<SALCTRTHKGILTFVQHFRSGLPKPA

Parental  FMKQNLDALGIG-TYHNI-AFIHPDTPIIKALNVFVERRVSALPVVDESGKVVDIYSKFDVINLAAEKTY
          FMKQNLD.L..G...HNI..FI...TPI..AL..FVER...A..VV.ESG..VDIYSK.D.I.LA.EKT.
Retrocopy FMKQNLDVLAFG<AHHNI<PFILQETPISTALKIFVERQLLAFLVVNESGEIVDIYSKSDLIKLAVEKTF

Parental  NNLD-ITVTQAL-QHRSQYFEGVVKCSKLEILETIVDRIVRAEVHRLVVVNEADSIVGIISLSDILQALI
          .NL..ITVTQAL.QH.SQ..EGVV....LEIL.....R...A....LV...EADSI.G.ISL.D...ALI
Retrocopy SNLE<ITVTQAL<QHCSQCLEGVVMYGNLEILD----RLAWADLGLLV-ASEADSIMGVISLPDVW*ALI

Parental  LTPAGAKQKEAEAE
          L.PAGAKQKE.EAE
Retrocopy LMPAGAKQKETEAE

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_1890 retrocopy.

TSS

Ailuropoda melanoleuca was not studied using FANTOM5 data.

Lab

retro_amel_1890 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 4 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000006964	2 retrocopies	retro_amel_1722, retro_amel_406,
Ailuropoda melanoleuca	ENSAMEG00000013406	1 retrocopy	retro_amel_1890 ,
Felis catus	ENSFCAG00000003842	2 retrocopies	retro_fcat_237, retro_fcat_240,
Otolemur garnettii	ENSOGAG00000008645	1 retrocopy	retro_ogar_201,