RetrogeneDB ID: retro_amel_663

Retrocopy location

• Organism: Panda (Ailuropoda melanoleuca)
• Coordinates: GL192557.1:175796..176586(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PPP2CB
• Ensembl ID: ENSAMEG00000001615
• Aliases: None
• Description: protein phosphatase 2, catalytic subunit, beta isozyme [Source:HGNC Symbol;Acc:9300]

Sequence

>retro_amel_663
GACAACTAGGTGTTCACCAAGGAGCTGCACCAGTGGGTTGAACAGCTGAATGATTATGAACAGCTTAATGAGAACCAAGT
GTGGTGCAGTACAAGAAGGCTAAGGAAATTTTCTCGGAAGAATCAAAAGTGCAAGAGGTTCATTGTCCTGTTACCCTGTG
TGGAGATGTGCATGGTCAATTCTTTGATATTATGGAGCTCTTTAGAATTGGTGGAAAATCACCAGGTAGAAACTATCTAT
TCATGGGCAACTGTGTAGACATAAGCTATACTCAGTGGAGACTGTGACTCTTCTTGTGGCCTTACAGGTGTGTTACCTGG
AGTGCATTACCATATTGAGAGGAAACCACGAAAGCCGATAGGTTACCCAAGTATATGGCTTCTGTGATGAACGTCTGTGA
AAGTATGGAAATGCCAAAGTGTGAAAATATTTTACAGATCTATTTGATCGTCTTCCAGTTAGAGCGTTAGTAGATGGACA
GATATTCAACCTCCATGGTGGCCCCTCTCCATTCCTAGATTCACTGGCTCATACAAGAGCCTTGAGTCATTTACAGGAAG
TTCCACAGGAGGGCCCATTGTGTGATCTGTAGTGGTCAGATCCAGAGGATCATGGCCGGTGGGATATTTCACCACCTAGT
GCTGGCTGTACGTTTGGACAAGACATTTCTGAAACACTTAACCAAACCAATGGTCTCACACTGGCTTCTCGAGCTCACCA
ACTTGTAATGGAGGAATACAGTTGGTGTCATGATCAGAATGTGGTGACCATTTTTAGTGCACCCAGTTAC

Alignment

ORF - retro_amel_663 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 73.68 %
• Parental protein coverage: 85.71 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  DDKAFTKELDQWVEQLNECKQLNENQVRTLCEK-AKEILTKESNVQEVRCPVTVCGDVHGQFHDLMELFR
          D...FTKEL.QWVEQLN...QLNENQV.......AKEI...ES.VQEV.CPVT.CGDVHGQF.D.MELFR
Retrocopy DN*VFTKELHQWVEQLNDYEQLNENQVWCSTRR<AKEIFSEESKVQEVHCPVTLCGDVHGQFFDIMELFR

Parental  IGGKSPDTNYLFMGDYVDRGY-YSVETVTLLVALKVRYPERITILRGNHESRQITQVYGFYDECLRKYGN
          IGGKSP..NYLFMG..VD..Y.YSVETVTLLVAL.V.Y.E.ITILRGNHESR..TQVYGF.DE.L.KYGN
Retrocopy IGGKSPGRNYLFMGNCVDISY<YSVETVTLLVALQVCYLECITILRGNHESR*VTQVYGFCDERL*KYGN

Parental  ANVWKYFTDLFDYLPLTALVDGQIFCLHGGLSPSIDTLDHIRALDRLQEVPHEGPMCDLLWSDPDDRGGW
          A.V.KYFTDLFD.LP..ALVDGQIF.LHGG.SP..D.L.H.RAL..LQEVP.EGP.CDL.WSDP.D.G.W
Retrocopy AKV*KYFTDLFDRLPVRALVDGQIFNLHGGPSPFLDSLAHTRALSHLQEVPQEGPLCDL*WSDPEDHGRW

Parental  GISPRGAGYTFGQDISETFNHANGLTLVSRAHQLVMEGYNWCHDRNVVTIFSAPNY
          .ISP..AG.TFGQDISET.N..NGLTL.SRAHQLVME.Y.WCHD.NVVTIFSAP.Y
Retrocopy DISPPSAGCTFGQDISETLNQTNGLTLASRAHQLVMEEYSWCHDQNVVTIFSAPSY

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_663 retrocopy.

TSS

Ailuropoda melanoleuca was not studied using FANTOM5 data.

Lab

retro_amel_663 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 9 parental genes, and 15 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000001615	1 retrocopy	retro_amel_663 ,
Ailuropoda melanoleuca	ENSAMEG00000015223	1 retrocopy	retro_amel_286,
Bos taurus	ENSBTAG00000009245	3 retrocopies	retro_btau_1199, retro_btau_1750, retro_btau_704,
Dasypus novemcinctus	ENSDNOG00000010906	1 retrocopy	retro_dnov_2211,
Echinops telfairi	ENSETEG00000018123	4 retrocopies	retro_etel_1607, retro_etel_1923, retro_etel_680, retro_etel_702,
Felis catus	ENSFCAG00000025139	1 retrocopy	retro_fcat_1884,
Monodelphis domestica	ENSMODG00000019001	2 retrocopies	retro_mdom_192, retro_mdom_632,
Otolemur garnettii	ENSOGAG00000002488	1 retrocopy	retro_ogar_3188,
Tursiops truncatus	ENSTTRG00000000102	1 retrocopy	retro_ttru_1576,