RetrogeneDB ID: retro_amel_954

Retrocopy location

• Organism: Panda (Ailuropoda melanoleuca)
• Coordinates: GL192767.1:1034886..1035387(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CCDC59
• Ensembl ID: ENSAMEG00000016875
• Aliases: None
• Description: coiled-coil domain containing 59 [Source:HGNC Symbol;Acc:25005]

Sequence

>retro_amel_954
GGCTTTGCATTTCAAAAAAACGGAAGATTCAGCAAAATTACAAGAGGTTGCTTTGGAAGGAAAAGAAGGTTCAAACCTCA
CAGGAATCCCTATTTGCAATTGGATGCCCTGACAACCCGAAACATCTCTAATTAGCTGAAGAGGAAAGGCTCAGGAAGCC
ACTTAGAAAAGTTAAGCAAGCTCTGTCAGCAGAACAAGGTGTTCAGCCGTTGCCAGAAGAACAAGGTATTACTGACCAGG
CTTTGTGTGACGCACACTGCAGAGTTGACCAGCCTCAGCCAGGACAGTGTAGCAAAAGTGCAGACCTCATTACTATTCCA
AAGAAAGATAAATCATCAAATGAACAAGCACAAGAAAAAGGTGAGCAAGTACAAGCTAAGTATGCTGCTAAGAAACAAGA
TTCTGAGAGGACAAAACGAGACAGACAAAGTTCAAAAGCTTTACAAAATGTAAAAAATGCAAGTGTTCAGAAGACTGAGC
AAAAAGACTAAAAAGGGCCAA

Alignment

ORF - retro_amel_954 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 56.32 %
• Parental protein coverage: 76.11 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  GFAFRR-KLKIQQNYRKLLWREKKAQTLQESQFTDRYPEHLKHLYLAEEKRLRKPLRKVEQPLSKELADQ
          GFAF...K.KIQQNY..LLW.EKK.QT.QES.F....P...KHL.LAEE.RLRKPLRKV.Q.LS.E...Q
Retrocopy GFAFQK<KRKIQQNYKRLLWKEKKVQTSQESLFAIGCPDNPKHL*LAEEERLRKPLRKVKQALSAEQGVQ

Parental  PLPKEQCDIDQALSEEHCSFEQPQSAEQCSIRINSITIISRKNKKKTSNQKAQEEYEQVQAERAAKKQEF
          PLP.EQ...DQAL...HC...QPQ...QCS.....ITI.....K.K.SN..AQE..EQVQA..AA.K...
Retrocopy PLPEEQGITDQALCDAHCRVDQPQPG-QCSKSADLITI---PKKDKSSNEQAQEKGEQVQAKYAA-KKQD

Parental  EKR-KQEREEAQRLYKKKKMETFKILSKKTKKGQ
          ..R...E....Q.LYK..KM..F..LSKKTKKGQ
Retrocopy SER>QNETDKVQKLYKM*KMQVFRRLSKKTKKGQ

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_954 retrocopy.

TSS

Ailuropoda melanoleuca was not studied using FANTOM5 data.

Lab

retro_amel_954 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 12 parental genes, and 27 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000016875	1 retrocopy	retro_amel_954 ,
Bos taurus	ENSBTAG00000036282	4 retrocopies	retro_btau_725, retro_btau_726, retro_btau_727, retro_btau_728,
Choloepus hoffmanni	ENSCHOG00000007788	1 retrocopy	retro_chof_1648,
Dasypus novemcinctus	ENSDNOG00000011546	1 retrocopy	retro_dnov_1033,
Dipodomys ordii	ENSDORG00000003005	1 retrocopy	retro_dord_485,
Echinops telfairi	ENSETEG00000000256	2 retrocopies	retro_etel_1338, retro_etel_1789,
Gorilla gorilla	ENSGGOG00000025296	2 retrocopies	retro_ggor_1386, retro_ggor_99,
Microcebus murinus	ENSMICG00000000967	4 retrocopies	retro_mmur_1456, retro_mmur_354, retro_mmur_689, retro_mmur_909,
Oryctolagus cuniculus	ENSOCUG00000017824	2 retrocopies	retro_ocun_1782, retro_ocun_498,
Otolemur garnettii	ENSOGAG00000004383	1 retrocopy	retro_ogar_2065,
Pan troglodytes	ENSPTRG00000005266	1 retrocopy	retro_ptro_1270,
Tupaia belangeri	ENSTBEG00000008887	7 retrocopies	retro_tbel_1515, retro_tbel_2047, retro_tbel_2126, retro_tbel_302, retro_tbel_3391, retro_tbel_3721, retro_tbel_972,