RetrogeneDB ID: retro_amel_1722

Retrocopy location

• Organism: Panda (Ailuropoda melanoleuca)
• Coordinates: GL194092.1:129878..130517(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PRKAG1
• Ensembl ID: ENSAMEG00000006964
• Aliases: None
• Description: protein kinase, AMP-activated, gamma 1 non-catalytic subunit [Source:HGNC Symbol;Acc:9385]

Sequence

>retro_amel_1722
TTGGCTACTAATGGTATATGAGCTGCCCCTTTGTGGGAAAGTACGAAGCAAAGTTTTGTGGGCATGCTGGCCATCAAGGA
TTCCGTCAATATCCTGCAGTTACTAATAAACCAGTCTTGGTATAGATCTATGAGCTGGAAGAATGCGAGACAGAAACCTG
GAGGGAAGTGTATCCACAGGATTTCTTTAATCCCTTGTCTACATTGCTTCTAATGTCAGCTTGTTTAATGCTGTCTCTTC
ATTAATTCAAAATAAGACCCACAGGCTGCCAGTTATTGACCTGGCATCAGGCAACATCTTGTACCTCTTCACCTATATGC
GCATTCTCAAGTTCTTCAAATCATTTGCCACTGTGTTTCCCAAGCCAGAGTTCATGTCTAAGTCTACGGAAGAGCTGTAG
ATTAGCATGTAGGCCAACACTGTTATGGGCCACACTACCACCCCTGTCCAGGTGGCTCTGGGCATTTTGTACAGCACTGA
TTCTCAGCCCTGCTGGTGGTGGATGAGAAAGAGTGTGTGGTGGACATCTACACCAAGTTTTAGGTTATCAATTTGGCAGC
AGAAAAGATCTACATTAACCTGGATGTGCCAGGGACCAAAGCTCTACAACGTTGATCACATTACTTTAAATGTGTCCTT

Alignment

ORF - retro_amel_1722 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 68.2 %
• Parental protein coverage: 65.05 %
• Number of stop codons detected: 7
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  LVTNGVRAAPLWDSKKQSFVGMLTITDFINILHRYY-KSALVQIYELEEHKIETWREVYLQDSFKPL-VC
          L.TNG..AAPLW.S.KQSFVGML.I.D..NIL.....K..LV.IYELEE...ETWREVY.QD.F.PL.V.
Retrocopy LATNGI*AAPLWESTKQSFVGMLAIKDSVNILQLLI<KPVLV*IYELEECETETWREVYPQDFFNPL<VY

Parental  ISPNASLFDAVSSLIRNKIHRLPVIDPESGNTLYILTHKRILKFLKLFITEFPKPEFMSKSLEELQIGTY
          I..N.SLF.AVSSLI.NK.HRLPVID..SGN.LY..T..RILKF.K.F.T.FPKPEFMSKS.EEL.I...
Retrocopy IASNVSLFNAVSSLIQNKTHRLPVIDLASGNILYLFTYMRILKFFKSFATVFPKPEFMSKSTEEL*ISM*

Parental  ANIAVVRTTTPVYVALGI-FVQHRVSALPVVDEKGRVVDIYSKFDVINLAAEKTYNNLDVSVTKALQHRS
          AN.....TTTPV.VALGI.FVQH..SAL.VVDEK..VVDIY.KF.VINLAAEK.Y.NLDV..TKALQ..S
Retrocopy ANTVMGHTTTPVQVALGI<FVQH*FSALLVVDEKECVVDIYTKF*VINLAAEKIYINLDVPGTKALQR*S

Parental  HYFEGVL
          HYF..VL
Retrocopy HYFKCVL

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_1722 retrocopy.

TSS

Ailuropoda melanoleuca was not studied using FANTOM5 data.

Lab

retro_amel_1722 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 9 parental genes, and 12 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,
Choloepus hoffmanni	ENSCHOG00000006397	1 retrocopy	retro_chof_32,
Callithrix jacchus	ENSCJAG00000020827	2 retrocopies	retro_cjac_3045, retro_cjac_3892,
Felis catus	ENSFCAG00000000091	1 retrocopy	retro_fcat_1730,
Myotis lucifugus	ENSMLUG00000011156	2 retrocopies	retro_mluc_2417, retro_mluc_451,
Oryctolagus cuniculus	ENSOCUG00000008409	1 retrocopy	retro_ocun_829,
Sus scrofa	ENSSSCG00000000185	1 retrocopy	retro_sscr_210,
Tursiops truncatus	ENSTTRG00000004730	1 retrocopy	retro_ttru_497,