RetrogeneDB ID: retro_amel_321

Retrocopy location

• Organism: Panda (Ailuropoda melanoleuca)
• Coordinates: GL192385.1:1490904..1491917(+)
• Located in intron of: ENSAMEG00000002723

Retrocopy information

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

Parental gene information

• Parental gene symbol: PLIN2
• Ensembl ID: ENSAMEG00000002827
• Aliases: None
• Description: perilipin 2 [Source:HGNC Symbol;Acc:248]

Sequence

>retro_amel_321
AGGATTGGGGAGAAACTGCCTGTTCTGAATCAGCTGATGAACCAGCCAACAAACCAGGTTGTTACCAATGGCAGAGGTGA
TATGACCAGGGCAAAAGATGCTGTGACAACTACTGTGACCGGGGCCAAGGATTCCATGGCCAGCACCGTCACTGGAGTAA
TGGACAAGACCAAAGGAGCGGTGACTGGCAGTGTGGAGAAGACCAAGGCTATGGTCAATGGCAGCATTAACACAGTCTTG
GGAGGTCAGATGATGCAGCTGGTGAGCAGCGGAGTAGAAAATGCGCTCACCAAATCAGAGCTGCTGGTGGATCAGTACCT
CCCTCTCACGGAGAAAGAACTAGAAAAAGAAGCAAAAAAAGTTGAAGGGTTTGATACGGTTCAGAAGCCAAGTTATTACA
TTAGACTGGGATCCCTGTCTACCAAGCTCCGCTCCCATGTCTACCAGCAAGCTCTCAGCGGGGTTAAAGAAGCCAAGCAA
AAAAGCCAAGAGACCATTTCTCAGCTCCATTCCACTGTTAATCTGATTGAATTTGCCAGGAAGAATGTGCACAGTGCCAA
CTGGAAAATTCAAGGTGCTCAGGATAAGTTCTCTCTCTCCCAGGTGGAGTGGAAGAGAAGCATTGGCCATGATGGTACAG
AAGAATGCCACTGTGCTGAGCACTTTGAGTCCCGTCCTCTCGCGATTGCCCACAACCTGACCCAGCAGCTCCAGACCACG
TGCCACACCCTGCCGTCCAGTATCCCAGGGTTACCACAGAACCTCCAAGATCAGGCCAGTCCCTTGGGTGCCATCGACTC
AGGGTTCCGCCATGCTGCCTCCTTCAAGGAAGTGTCTGACGGCCTCCTCACTTCCCGCAAGGGGCAGCTGCAGAAAATGA
AGGAGTCTTTAGATGATATGATGGCTTATCTTATTAACTACATGCCTCTCAGAGGCTGGTAGACCCCTTTGACCTGCAGC
TGACCGAGTCTCAGAACGCTCAGGACCAAGGTGCACAGGAGGCCACGAGCAGT

Alignment

ORF - retro_amel_321 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 82.22 %
• Parental protein coverage: 75.11 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  RIEEKLP----ILNRPTNQVVASARGAMTGAKDAVTTTVTGAKDSVASTITGVMDKTKGAVTGSVEKTKA
          RI.EKLP......N.PTNQVV...RG.MT.AKDAVTTTVTGAKDS.AST.TGVMDKTKGAVTGSVEKTKA
Retrocopy RIGEKLPVLNQLMNQPTNQVVTNGRGDMTRAKDAVTTTVTGAKDSMASTVTGVMDKTKGAVTGSVEKTKA

Parental  MVNGSINTVLGSRVMQLVSSGVENALTKSELLVDQYLPLTEKELEKEAKKVEGFDTVQKPSYYIRLGSLS
          MVNGSINTVLG...MQLVSSGVENALTKSELLVDQYLPLTEKELEKEAKKVEGFDTVQKPSYYIRLGSLS
Retrocopy MVNGSINTVLGGQMMQLVSSGVENALTKSELLVDQYLPLTEKELEKEAKKVEGFDTVQKPSYYIRLGSLS

Parental  TKLRSRAYQQALGRVKEAKQKSQETISQLHSTVNLIEFARKNVHSANQKIQGAQDKFHLSWVEWKRSIGY
          TKLRS..YQQAL..VKEAKQKSQETISQLHSTVNLIEFARKNVHSAN.KIQGAQDKF.LS.VEWKRSIG.
Retrocopy TKLRSHVYQQALSGVKEAKQKSQETISQLHSTVNLIEFARKNVHSANWKIQGAQDKFSLSQVEWKRSIGH

Parental  DDTDESHCAEHIESRTLAIARNLTQQLQTTCHTLLSSIQGLPQNVQDQASHLGVMASDIYSGFRHASSFR
          D.T.E.HCAEH.ESR.LAIA.NLTQQLQTTCHTL.SSI.GLPQN.QDQAS.LG...S....GFRHA.SF.
Retrocopy DGTEECHCAEHFESRPLAIAHNLTQQLQTTCHTLPSSIPGLPQNLQDQASPLGAIDS----GFRHAASFK

Parental  EVSDGLLTSSKGQLQKMKESLDDVMDYLVNNTPLNW-LVGPFYPQLTESQNAQDQGAVRRPSS
          EVSDGLLTS.KGQLQKMKESLDD.M.YL.N..PL...LV.PF..QLTESQNAQDQGA....SS
Retrocopy EVSDGLLTSRKGQLQKMKESLDDMMAYLINYMPLRG<LVDPFDLQLTESQNAQDQGAQEATSS

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_321 retrocopy.

TSS

Ailuropoda melanoleuca was not studied using FANTOM5 data.

Lab

retro_amel_321 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 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000002827	1 retrocopy	retro_amel_321 ,
Callithrix jacchus	ENSCJAG00000008088	1 retrocopy	retro_cjac_2494,
Latimeria chalumnae	ENSLACG00000017943	1 retrocopy	retro_lcha_61,