RetrogeneDB ID: retro_amel_1845

Retrocopy location

• Organism: Panda (Ailuropoda melanoleuca)
• Coordinates: GL194764.1:10848..11630(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSAMEG00000005268
• Aliases: None
• Description: None

Sequence

>retro_amel_1845
AGCCAAGCCATAACCAATGAATATGAAGTGCAGAGAAAGCTGCTAGTAAAACGTTTGGATGTCACTGTCTAGGCTTTTGG
CTGGTCTTACAGAGCTGAGTCAGAGAGAAAAATTAGCAAAGGTTTACCAGCTGAAATGCTCAGTTTTATCTCCTAAAAGT
CTTGTTTCTGTTGTCCACATTTGACTGCAAGGTAAGACTTGTTGAAGATTTTAAGGACAAGCAGTGACTATATAAGAGAA
AATGTTGCCTGTGCCATCAATAAGGTGTTGATGGGCAGGGTGTCTGACAGAGGGGTAGAACCAATGAAATTAAACCTGCA
CCTTCAGAGATGCCACCATTTTGGAAAGGGCGAGATTACCCTGAAGTAGCAACGAGGAGCCTAAGGAGGAGGAAGAGGTG
ATTATGAATATTCCTCATATGAAGGTGGAGAAGGTCATGAACAAGGAGGAGGGAGTGGTGGATGTGGTAGCTATGACCAT
GGTCGCCGAAGGGGAAGAAGAGGAAATAAACATCAAGGAGGCTGGATGGTGGCTAGCAAGATGGTGGTTATTGAGATTCA
GGTTTCTAGTCAGGTGGCTATCAAGGTGGTGCCCATCGTGGTAGATATCAAGGCGGTGGTTATGGTGGCTTCCAAACATC
TACATATGCAAGAAATGAATACAAAAGTGGTGGATACCAGCAGGACAAAAGATACCAAGATGATGGACAGTGGTCATTGA
GGGAGAGGTGTTCATGGGGCCGATGTAGATATGGTGGCCAAGGAAGAGGCTGGGGAGGAAGG

Alignment

ORF - retro_amel_1845 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 61.68 %
• Parental protein coverage: 51.84 %
• Number of stop codons detected: 6
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  NQAIANEYEVRRKLLIKRLDVTVQSFGWSDRAKSQTEKLA-KVYQPKRSVLSPKSTISVAHL-LAARQDL
          .QAI.NEYEV.RKLL.KRLDVTV..FGWS.RA.S...K...KVYQ.K.SVLSPKS..SV.H..L.AR.DL
Retrocopy SQAITNEYEVQRKLLVKRLDVTV*AFGWSYRAESE-RKIS>KVYQLKCSVLSPKSLVSVVHI<LTAR*DL

Parental  SKILRTSSGSIREKTACAINKVLMGRVPDRG-GRPNEIEPPPPEMPPWQKRQDGPQQ-QTGGRGGGRGGY
          .KILRTSS..IRE..ACAINKVLMGRV.DRG.GR.NEI.P.P.EMPP..K..D.P...Q.G..GGGRG.Y
Retrocopy LKILRTSSDYIRENVACAINKVLMGRVSDRG<GRTNEIKPAPSEMPPFWKGRDYPEV>QRGA*GGGRGDY

Parental  EHSSYGGRGGHEQGGGRGGRGGYDHGSRGGGRGNKHQGGW-TDGGSGGGGGYQDGGYRDSGFQPGGYHGG
          E.SSY.G..GHEQGGG.GG.G.YDHG.R.G.RGNKHQGGW...G...GG..Y.D.G....G.Q.GG.H.G
Retrocopy EYSSYEGGEGHEQGGGSGGCGSYDHGRRRGRRGNKHQGGW<DGG*QDGG--Y*DSGF*SGGYQ-GGAHRG

Parental  GHSGSYQGGGYGGFQTSTYTGSGYQGGGYQQDNRYQDGGHHNDRGSGRGGRGGRGGRG-GRGGQ
          ...G....GGYGGFQTSTY....Y..GGYQQD.RYQD.G....R.....GR...GG.G.G.GG.
Retrocopy RYQG----GGYGGFQTSTYARNEYKSGGYQQDKRYQDDGQWSLRERCSWGRCRYGGQGRGWGGR

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_1845 retrocopy.

TSS

Ailuropoda melanoleuca was not studied using FANTOM5 data.

Lab

retro_amel_1845 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 5 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000005268	2 retrocopies	retro_amel_1607, retro_amel_1845 ,
Choloepus hoffmanni	ENSCHOG00000000476	1 retrocopy	retro_chof_691,
Callithrix jacchus	ENSCJAG00000003525	1 retrocopy	retro_cjac_510,
Mustela putorius furo	ENSMPUG00000010098	1 retrocopy	retro_mputfur_1193,
Rattus norvegicus	ENSRNOG00000030328	1 retrocopy	retro_rnor_614,