RetrogeneDB ID: retro_amel_1888

Retrocopy location

• Organism: Panda (Ailuropoda melanoleuca)
• Coordinates: GL195245.1:12587..13540(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CSNK2A3
• Ensembl ID: ENSAMEG00000014039
• Aliases: None
• Description: casein kinase 2, alpha 3 polypeptide [Source:HGNC Symbol;Acc:2458]

Sequence

>retro_amel_1888
AGCAGGGCCCAGGTCTAAGCCTAGGTGAAATGCTTGAGGAGCAGCGAGTACTGGGACTATGAGGCTCACGTCCGAGCTGG
GGTAATCAAGATGATTACCAACTGGTTTGAAAACTTGGTTGGGGAAAGTATAGTGAAGTATTTGAGGCCATTAACATCAC
CAACAATGAGAGAGTGGTTGTAAAAATTCTCAAGCCAGTGAAGAAAAAGAAGATAGAAGGAGAGGTTAAGATTCTGGAGA
ACCTTCATGGTGGAACAAATATCATTAAGCTGATTGACACTGTGAAGGACCCTGTGTCAAAGACACCAGCTTTGGTATTT
GAATATATCAATAATACAGATTTTAAGCAACTTTACCAGATCCTGACAGACTTCGATATCTGGTTTTATATGTATGAGCT
ACTTAAGGCTCTGGATTACTGCCACAGCAAGGGAATCATGCACAGGGATGTGAAACCTCACAATCTCATGATAGATCACC
AACAGCAAAAGCCTGGACTGATAAACTGGGGTCTGGCAGAGTTCTACCATCCTGCTCAGGAGTACAATGTCCGTGTAGCC
TCAAGGTACTTCAAGGGCCCGGAGCTCCTCGTGGACTATCAGATATATGATTACAGCTTGGACATGTGGAGTTTGGGCTG
TATGTTAGCAAGCATGATCTTTTGAAAGGAGCCCTTCTTTCACGGACAGGACAACTATGACCAGCTTGTTCGCATTGCCA
AGGTTCTGGGTACAGATGAGCTGTATGGGTATCTGAAGAAGTATCACATAGACCTAGATCCGCACTTCAACGATATCCTG
GGACAACATTCACGGAAACGCTGGGAAAACATTATCCATAGTGAGAACAGACACCTCGTCAGCCCCGAGGCCCTAGATCT
TCTGGACAAACTTCTGCGATACGACCATCAACAGAGACTGACTGCCAAAGAGGCCATGGAGCACCCGTACTTC

Alignment

ORF - retro_amel_1888 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 81.5 %
• Parental protein coverage: 80.51 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  SRARVYTDVNTHRPREYWDYESHV-VEWGNQDDYQLVRKLGRGKYSEVFEAINITNNEKVVVKILKPVKK
          SRA.V...V...R..EYWDYE.HV...WGNQDDYQLV.KLG.GKYSEVFEAINITNNE.VVVKILKPVKK
Retrocopy SRAQV*A*VKCLRSSEYWDYEAHV<PSWGNQDDYQLV*KLGWGKYSEVFEAINITNNERVVVKILKPVKK

Parental  KKIKREIKILENLRGGPNIITLADIVKDPVSRTPALVFEHVNNTDFKQLYQTLTDYDIRFYMYEILKALD
          KKI..E.KILENL.GG.NII.L.D.VKDPVS.TPALVFE..NNTDFKQLYQ.LTD.DI.FYMYE.LKALD
Retrocopy KKIEGEVKILENLHGGTNIIKLIDTVKDPVSKTPALVFEYINNTDFKQLYQILTDFDIWFYMYELLKALD

Parental  YCHSMGIMHRDVKPHNVMIDHEHRKLRLIDWGLAEFYHPGQEYNVRVASRYFKGPELLVDYQMYDYSLDM
          YCHS.GIMHRDVKPHN.MIDH...K..LI.WGLAEFYHP.QEYNVRVASRYFKGPELLVDYQ.YDYSLDM
Retrocopy YCHSKGIMHRDVKPHNLMIDHQQQKPGLINWGLAEFYHPAQEYNVRVASRYFKGPELLVDYQIYDYSLDM

Parental  WSLGCMLASMIFRKEPFFHGHDNYDQLVRIAKVLGTEDLYDYIDKYNIELDPRFNDILGRHSRKRWERFV
          WSLGCMLASMIF.KEPFFHG.DNYDQLVRIAKVLGT..LY.Y..KY.I.LDP.FNDILG.HSRKRWE...
Retrocopy WSLGCMLASMIF*KEPFFHGQDNYDQLVRIAKVLGTDELYGYLKKYHIDLDPHFNDILGQHSRKRWENII

Parental  HSENQHLVSPEALDFLDKLLRYDHQSRLTAREAMEHPYF
          HSEN.HLVSPEALD.LDKLLRYDHQ.RLTA.EAMEHPYF
Retrocopy HSENRHLVSPEALDLLDKLLRYDHQQRLTAKEAMEHPYF

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_1888 retrocopy.

TSS

Ailuropoda melanoleuca was not studied using FANTOM5 data.

Lab

retro_amel_1888 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 14 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000014039	2 retrocopies	retro_amel_138, retro_amel_1888 ,
Homo sapiens	ENSG00000101266	1 retrocopy	retro_hsap_53,
Sorex araneus	ENSSARG00000002896	10 retrocopies	retro_sara_188, retro_sara_189, retro_sara_240, retro_sara_357, retro_sara_468, retro_sara_508, retro_sara_534, retro_sara_572, retro_sara_738, retro_sara_755,
Tursiops truncatus	ENSTTRG00000007064	1 retrocopy	retro_ttru_1605,