RetrogeneDB ID: retro_amel_1272

Retrocopy location

• Organism: Panda (Ailuropoda melanoleuca)
• Coordinates: GL193133.1:457048..457512(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSAMEG00000001600
• Aliases: None
• Description: None

Sequence

>retro_amel_1272
TATCAGGTGACAGGTGAAAACTAGAAGTCAAGTGGTGGCCATGAACTTGGGGCTGATGAAGATTTGGTGCTTGAAAATGA
GAGTCAGACGTCTTTTAAAACACAAGCAGAGAAACAGCAAAGAAAGGGAACTTGCCTAAGACTTTAACCAACATTTCACT
CTCTGTTGAGCAGCTCACGCAGAAAGAGGTTCTTGATCTTCCTGGAGAACCTCCTGAAACAGCCGAACAAGTAGGTGCTG
TTGCTCCGCGGTGTCCCAATGGGAGTGTCCTGAGAAGATTTTTTAAGTCTTGCAGTTCACAGGTCTAATTTCACTGGGTG
ATGAAAATCGGGTACCACACATCCCTATACAGCTTTTCTACTTCCTTTCCCAAAAGACCTCTGGAACTGGAGGAAGGCTG
GTCACTGCAGAACATAGGAATAACTATGGATATTGTACTCAATGTGGAAAAGAAAGAGCAGAGC

Alignment

ORF - retro_amel_1272 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 72.78 %
• Parental protein coverage: 56.47 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  YQMTGETWKLSNGHKLGQGDEDLVLEDGSQTSFETP-NREAAKRRNLPKPVTRISASAEQPTQKEVLDLP
          YQ.TGE..K.S.GH.LG..DEDLVLE..SQTSF.T...RE.AK..NLPK..T.IS.S.EQ.TQKEVLDLP
Retrocopy YQVTGEN*KSSGGHELG-ADEDLVLENESQTSFKTQ<SRETAKKGNLPKTLTNISLSVEQLTQKEVLDLP

Parental  EEPPETAEEVVTVALRCPSGSVLRRRFFKSCSSQVLFDWMMKIGYHTSRYSLSTSFPRRPLEMEGGWSLQ
          .EPPETAE.V..VA.RCP.GSVL.RRFFKSCSSQV.F.W.MKIGYHTS.YS.STSFP.RPLE.E.GWSLQ
Retrocopy GEPPETAEQVGAVAPRCPNGSVL-RRFFKSCSSQV*FHWVMKIGYHTSLYSFSTSFPKRPLELEEGWSLQ

Parental  DIGITVDTVLNVEEKEQT
          .IGIT.D.VLNVE.KEQ.
Retrocopy NIGITMDIVLNVEKKEQS

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_1272 retrocopy.

TSS

Ailuropoda melanoleuca was not studied using FANTOM5 data.

Lab

retro_amel_1272 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 3 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000001600	2 retrocopies	retro_amel_1272 , retro_amel_1326,
Choloepus hoffmanni	ENSCHOG00000006159	4 retrocopies	retro_chof_1161, retro_chof_1175, retro_chof_1383, retro_chof_1500,
Myotis lucifugus	ENSMLUG00000016846	1 retrocopy	retro_mluc_606,