RetrogeneDB ID: retro_amel_1607

Retrocopy location

• Organism: Panda (Ailuropoda melanoleuca)
• Coordinates: GL193726.1:49453..50717(+)
• 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_1607
ATGGAGTGTGACCTCATAGAGACTAGCATCTTGGAGTCGTTGGAAGATCTAGGTTACAAGGGTCCATTGTTGAAAGATGG
CGCTCTGTCTCAGGCAGCCTCTGCTGGAGCCGGTTCCCCCAAGTTTACCAAACTCTGTGCTTGGCTGGTGTCTGAATTAA
GAGTGTTCTATAAACTAGAAGAAAAATGTGCAAGCAACTAACAGCCCGAGTGAAGCTGAAGAATTCCAGCTTGAGGTAAG
TTGGCTACTAGGGGAGATGGACTGTCCATATATTTCACTGACATCTGGGGATGTGACCACTGCCTTCTCATTCAGAACTG
CCTCCTTTTGCTCACATTCCTCATCTCAGAACTAGAAACTTCCAGAATGTTCTGTATGAATACTCCTCCAGAAAAAGCTC
AAGAAGGAGGCGGTAGTGAGCTCTTTCAAGAGTTGAAAGGCATATGTACTGCTCTAGGAATGTCCAAAACTCCAGCCAAT
GTAACTATGTTCCAGTTCTTCAGTGGGATTGAAAAAAAAAATTAAAGGAGACATTAGCAAAAGTTCCGCTTAACCATGTG
GAAAGCCTTTATGTTAGAAGCCAATGGGACCAGCCCACTGGGAAAAGATAGAAGCAATTAACCAAGCCATAGCCGATGCA
TCTGAAGTTCTGAGAAAGCTGCTAATAAAAGTCTTGGATGTCACTGTCTAGTCTTTTGGTTGGTCTGACAGAGCTAAGAG
TCAGACAGAAAAAACAGCAAAGGTTTACCAGCTGAAATGCTCAGTACTATCTCCTAAAAGTACTATTTCCGTTCCCACCT
TTTGGCTACAAGACAAGACTCGTCAAAGATTTTAAGGACAAGCAGTAGCTCTACAAAAGAAAAGACTGTCTGTGCCATCA
ATAAAGTGTTGATGGGAAGATGCCTAACAGAGGAGGTAGACCCAATGAAATTGAACCGCCACCTCCAGAGATGCCACCAT
GGCAGCAAAGGTAAAATGGCCCCCAGCAGCAAGCAGGAGGCCAAGAAGAAGGGAGAGGTGGTTATGAACATTCCCCATAT
GGAGGACGAGGAGGTCATGAACAAGGAAGAGGGACAGGTGGATGTGGTGGCTACAACCATGGTAGCAAGAGGGAGGAAGA
GGAAATACGCATCAAGGGGGCTAGATGGTTGGAGGGAGTGGAGGAGGAGGTGGTGGCTACCAAGCTGGTGGTCTTTGAGA
TTCGGGTTTCCAGCCAGGTGGCTACCACAGTGGTAGCTGTCAAGGTGGTGGTTATGGTGGCTTC

Alignment

ORF - retro_amel_1607 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 78.75 %
• Parental protein coverage: 82.4 %
• Number of stop codons detected: 6
• Number of frameshifts detected: 6

Retrocopy - Parental Gene Alignment:

Parental  MECDLMETDILESLEDLGYKGPLLEDGALSQAVSAGASSPEFTKLCAWLVSELRVFCKLEE-NVQATNSP
          MECDL.ET.ILESLEDLGYKGPLL.DGALSQA.SAGA.SP.FTKLCAWLVSELRVF.KLEE.NVQATNSP
Retrocopy MECDLIETSILESLEDLGYKGPLLKDGALSQAASAGAGSPKFTKLCAWLVSELRVFYKLEE>NVQATNSP

Parental  SEAEEFQLEVSGLLGEMNCPYLSLTSGDVTKR-LLVQKNCLLLLTYLISELEAARMLCVNTPPKKAQEGG
          SEAEEFQLEVS.LLGEM.CPY.SLTSGDVT...LL.Q.NCLLLLT.LISELE..RM.C.NTPP.KAQEGG
Retrocopy SEAEEFQLEVSWLLGEMDCPYISLTSGDVTTA<LLIQ-NCLLLLTFLISELETSRMFCMNTPPEKAQEGG

Parental  GSEVFQELKGICIALGMSKPPANITMFQFFSGI-EKKLKETLAKVPPNHVGKPLLKKPMGPAHWEKIEAI
          GSE.FQELKGIC.ALGMSK.PAN.TMFQFFSGI.....K....K......GKPL..KPMGPAHWEKIEAI
Retrocopy GSELFQELKGICTALGMSKTPANVTMFQFFSGI>XXXXKGDISKSSA*PCGKPLC*KPMGPAHWEKIEAI

Parental  NQAIANEYEVRRKLLIKRLDVTVQSFGWSDRAKSQTEKLAKVYQPKRSVLSPKSTISV-AHLLAARQDLS
          NQAIA...EV.RKLLIK.LDVTV.SFGWSDRAKSQTEK.AKVYQ.K.SVLSPKSTISV..HLLA.RQD.S
Retrocopy NQAIADASEVLRKLLIKVLDVTV*SFGWSDRAKSQTEKTAKVYQLKCSVLSPKSTISV<SHLLATRQDSS

Parental  KILRTSSGSIREKTACAINKVLMGR-VPDRGGRPNEIEPPPPEMPPWQKRQDGPQQQTGGRGGGRGGYEH
          KILRTSS.S..EKT.CAINKVLMGR..P.RGGRPNEIEPPPPEMPPWQ.R..GPQQQ.GG...GRGGYEH
Retrocopy KILRTSSSSTKEKTVCAINKVLMGR<MPNRGGRPNEIEPPPPEMPPWQQR*NGPQQQAGGQEEGRGGYEH

Parental  SSYGGRGGHEQGGGRGGRGGYDHGSR-GGGRGNKHQGGWTDGGS-GGGGGYQDGGYRDSGFQPGGYHGGG
          S.YGGRGGHEQG.G.GG.GGY.HGS...GGRGN.HQGG...GGS.GGGGGYQ.GG..DSGFQPGGYH.G.
Retrocopy SPYGGRGGHEQGRGTGGCGGYNHGSK<EGGRGNTHQGG*MVGGSGGGGGGYQAGGL*DSGFQPGGYHSG-

Parental  HSGSYQGGGYGGF
          ...S.QGGGYGGF
Retrocopy ---SCQGGGYGGF

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_1607 retrocopy.

TSS

Ailuropoda melanoleuca was not studied using FANTOM5 data.

Lab

retro_amel_1607 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,