RetrogeneDB ID: retro_amel_1525

Retrocopy location

• Organism: Panda (Ailuropoda melanoleuca)
• Coordinates: GL193554.1:422980..423539(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CDK2
• Ensembl ID: ENSAMEG00000003168
• Aliases: None
• Description: cyclin-dependent kinase 2 [Source:HGNC Symbol;Acc:1771]

Sequence

>retro_amel_1525
GTGGACAAGATCAGAGAGGGCACATATGGAGATGTGTACAAAGCCAAAAACAAGGTGACAGGAGAAGTGGTGGGGATTAA
AAAAATCCTTCTGGAAACTGAGACAAACAGTGTACCAGTACTGCTGTAGGAGAGAGATCTCTCTGTTTAAGGAGCTTAAC
CTCCTTCACATTGTCACGCTGCTGGATGTCATGCACACGGAAAACGAACTCTACCTGCTTTTTGAGTTTTTGCTCCAGGA
TCTGAAGAAATTCTTGGATGTCTCTGCTTTGACGGGCATTCCTCTTCCACTCATCATGAGTTGTCTGTTCCAGCTGCTCC
AGGGTCTAGCTTTCTGCCATTCTCATCTGATTCTGCATCAAGACCTCAGACCTCAAAATCTGCTTATCAACGCAGAGAGG
GCCATGAAGCTAGTAGACTTTGGACTAGCCAGAGCCTTTGGAGTCCCTGTTTGTACTTATACTCATGAGGTGGTGACCCT
GTGGAACCGAGCACCTGAAATTCTTCTGGGCTCCAAGTATTACTCCACAGCTGTAGATAACTGGAGCCTGGGCTGCTTG

Alignment

ORF - retro_amel_1525 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 78.31 %
• Parental protein coverage: 62.42 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  VEKIGEGTYGVVYKAKNKVTGEVVALKKIRLDTETEGVP-STAIREISL-LKEL-NHPNIVKLLDVIHTE
          V.KI.EGTYG.VYKAKNKVTGEVV..KKI.L.TET..VP.STA..E.SL.L..L.N...IV.LLDV.HTE
Retrocopy VDKIREGTYGDVYKAKNKVTGEVVGIKKILLETETNSVP<STAVGERSLCLRSL<NLLHIVTLLDVMHTE

Parental  NKLYLVFEFLHQDLKKFMDASALTGIPLPLIKSYLFQLLQGLAFCHSHRVLHRDLKPQNLLINAEGAIKL
          N.LYL.FEFL.QDLKKF.D.SALTGIPLPLI.S.LFQLLQGLAFCHSH..LH.DL.PQNLLINAE.A.KL
Retrocopy NELYLLFEFLLQDLKKFLDVSALTGIPLPLIMSCLFQLLQGLAFCHSHLILHQDLRPQNLLINAERAMKL

Parental  ADFGLARAFGVPVRTYTHEVVTLWYRAPEILLGCKYYSTAVDIWSLGCI
          .DFGLARAFGVPV.TYTHEVVTLW.RAPEILLG.KYYSTAVD.WSLGC.
Retrocopy VDFGLARAFGVPVCTYTHEVVTLWNRAPEILLGSKYYSTAVDNWSLGCL

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_1525 retrocopy.

TSS

Ailuropoda melanoleuca was not studied using FANTOM5 data.

Lab

retro_amel_1525 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.

---

Parental genes homology:

Parental genes homology involve 5 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000003168	1 retrocopy	retro_amel_1525 ,
Bos taurus	ENSBTAG00000004021	1 retrocopy	retro_btau_1424,
Erinaceus europaeus	ENSEEUG00000014081	1 retrocopy	retro_eeur_445,
Pteropus vampyrus	ENSPVAG00000007555	1 retrocopy	retro_pvam_794,
Tupaia belangeri	ENSTBEG00000005123	1 retrocopy	retro_tbel_4151,