RetrogeneDB ID: retro_amel_1840

Retrocopy location

• Organism: Panda (Ailuropoda melanoleuca)
• Coordinates: GL194707.1:73394..74420(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: TDP1
• Ensembl ID: ENSAMEG00000001905
• Aliases: None
• Description: tyrosyl-DNA phosphodiesterase 1 [Source:HGNC Symbol;Acc:18884]

Sequence

>retro_amel_1840
AAAATGATGTTACTACTGTATGAAGAAGGCCCTCTGGGTTGTCATACACACTTCCGACCTCATCCATGCTGACTGTCACC
AGAAAACTCAGGGAGAATGGTTGACCCCTTTATACCCACGGATTATCCATGGAACCACAGATCTGGAGAATCAGCAACAC
ATTTTAAAGCTGATCTCATCAGCTACTTGATGGCTTATAATGCTCCTTCACTCAAGGAGTGGATAGATACTGTCCACAAG
CATGATATCTCTGAAACCAATGTTTATCTTATTGGATCAACTCCAGGATGCTTTCAAGGAAGTCGAAAAGATCACTAGGG
ACATTTTAGGCTTAGAAAGCTCCTGAAAGAGCATGCCTCATCCATACCTAAAGGAGAGTCTTGGCCAATAGTAGGTCAGT
TTTCAAGCATTGGGTCTTTGGGAGCTGATGACTTGAAATGGCTGTGTTCTGAGTTTAAAGAAAGCTTGGCGACACTGGGG
AAGGAAAGCAGGACCCCAGGGAAAAGTGCTGTTCCTCTTCACCTGATCTATCCTTCTGTGGAAAACGTGCAAACCAGCTT
AGAAGAATATCCAGCTGGGGACTCTCTTCCCTCTAGCATCCAGATAGCTGAAAAACAGAATTGTCTCCATTCCTATTTTC
ACAAACGGTAGCTGACACATCTGGCTGCAACAATGCTATGCCACATATTAAAAGATATATGAGACCTTCTCCAGACTTCA
GTCAAATTGTTTGGTTGCTTGTCACAAGCACAAATCTGTCCAAGACCACCTAGGGAGCATTAGAGAAGAACGGCAACAGC
TGATGATCCATTCCTATGAGCTGGGGTCCTTTTCCTGCTGTCAGCATTTGGCCTGGACAGCTTCAAAGTAAAACAGAAAT
TATCAGGGAGCAAGGAGCCAGCAGCCACTTTTCCTGTGCCATATGACCTGCCTCCAGAACTGTATGGAAGTAAAGATCGG
CCATGAATTTAGAACATTCCTTATACCAAAGTACCAGATACACATGGGAATATGTGGGTTCCCTCC

Alignment

ORF - retro_amel_1840 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 83.71 %
• Parental protein coverage: 81.09 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  KMMLLLYEEG-LRVVIHTSNLIHADWHQKTQGIWLSPLYPPIIHGT-HRSGESTTHFKADLISYLMAYNA
          KMMLLLYEEG.L.VVIHTS.LIHAD.HQKTQG.WL.PLYP.IIHGT.HRSGES.THFKADLISYLMAYNA
Retrocopy KMMLLLYEEG>LWVVIHTSDLIHADCHQKTQGEWLTPLYPRIIHGT<HRSGESATHFKADLISYLMAYNA

Parental  PSLKEWIDIIHEHDLSETNVYLIGSTPGRFQGSQKDNWGHFRLRKLLKEHAS--PKGESWPVVGQFSSIG
          PSLKEWID..H.HD.SETNVYLIGSTPG.FQGS.KD..GHFRLRKLLKEHAS..PKGESWP.VGQFSSIG
Retrocopy PSLKEWIDTVHKHDISETNVYLIGSTPGCFQGSRKDH*GHFRLRKLLKEHASSIPKGESWPIVGQFSSIG

Parental  SMGADDSKWLCSEFKESLVTLGKESQTPGRSAVPLHLIYPSVENVRTSLEGYPEAGGSLPYSIQTAEKQN
          S.GADD.KWLCSEFKESL.TLGKES.TPG.SAVPLHLIYPSVENV.TSLE.YP.AG.SLP.SIQ.AEKQN
Retrocopy SLGADDLKWLCSEFKESLATLGKESRTPGKSAVPLHLIYPSVENVQTSLEEYP-AGDSLPSSIQIAEKQN

Parental  WLHSYFHK-WSADTSGRSNAMPHIKTYMRPSPDFSEIAWFLVTSANLSKAAWGALEKNGT-QLMIRSYEL
          .LHSYFHK...ADTSG..NAMPHIK.YMRPSPDFS.I.W.LVTS.NLSK...GALEKNG..QLMI.SYEL
Retrocopy CLHSYFHK<TVADTSGCNNAMPHIKRYMRPSPDFSQIVWLLVTSTNLSKTT*GALEKNGN<QLMIHSYEL

Parental  -GVLFLPSAFGLDSFKVKQKFFFGSKEPAAAFPVPYDLPPELYGSKDRPWIWNIPYTKAPDTHGNMWVPS
          .GVLFL.SAFGLDSFKVKQK...GSKEPAA.FPVPYDLPPELYGSKDRP.I.NIPYTK.PDTHGNMWVPS
Retrocopy <GVLFLLSAFGLDSFKVKQK-LSGSKEPAATFPVPYDLPPELYGSKDRP*I*NIPYTKVPDTHGNMWVPS

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_1840 retrocopy.

TSS

Ailuropoda melanoleuca was not studied using FANTOM5 data.

Lab

retro_amel_1840 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 3 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000001905	1 retrocopy	retro_amel_1840 ,
Choloepus hoffmanni	ENSCHOG00000005456	1 retrocopy	retro_chof_791,
Tupaia belangeri	ENSTBEG00000002578	2 retrocopies	retro_tbel_1158, retro_tbel_4636,