RetrogeneDB ID: retro_amel_1751

Retrocopy location

• Organism: Panda (Ailuropoda melanoleuca)
• Coordinates: GL194202.1:112506..112976(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: NELL1
• Ensembl ID: ENSAMEG00000014727
• Aliases: None
• Description: NEL-like 1 (chicken) [Source:HGNC Symbol;Acc:7750]

Sequence

>retro_amel_1751
GAAAACAGTTCTGTCTGTTCCTGCAAGGACCAAAAGATATTCTGTCAATAGACAGCTTATGATTGCTAGAATCCAAATGT
TGACCTTTTCTGTTGCCCAAAGTGTGAGGCCAGGGTCACAAGTCTATATTTAGATCAAAATGGACACAAGCTCTATCAAA
GTGGAGACAATTGGACTTGCTGCCAGCTGGCAGCAGTGCTGGTGTCTGGAAGAAGAGGTAGATTACTGGCCACTTGCTCC
AGTTTGAGCTGTGAGTACACAGCCATCTTGGAAAGGCATTGATGTCCCCACTGTATCTGTGACCTAGTTGAAAACATTGC
CTATGACATCAGAAAAACTTGCCTGGATGGCCGTGGCATTTCAAGGCTTAGCAGCTCAGTGTGAACATGGCTGGATCTCC
TTGTACAACCTGCAAATGCAAGGATGGAAACGCCTGCTGTTCAGTGAATTTGGAGTGTTTTCATAATAAT

Alignment

ORF - retro_amel_1751 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 64.38 %
• Parental protein coverage: 58.89 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  KKSFLCALKDGKIFCRRTACDCRNPSVDLFCCPECDTRVTSQCLDQNGHKLYRSGDNWTHSCQQCRCLEG
          ..S..C..KD.KIFC..TA.DC.NP.VDLFCCP.C..RVTS..LDQNGHKLY.SGDNWT..........G
Retrocopy ENSSVCSCKDQKIFCQ*TAYDC*NPNVDLFCCPKCEARVTSLYLDQNGHKLYQSGDNWTCCQLAAVLVSG

Parental  EVDCWPLTCPNLSCEYTAILEGECCPRCVSDPCLADNIAYDIRKTCLDSYGISRLSGSVWT-MAGSPCTT
          .......TC..LSCEYTAILE...CP.C..D..L..NIAYDIRKTCLD..GISRLS.SV.T.MAGSPCTT
Retrocopy RRGRLLATCSSLSCEYTAILERH*CPHCICD--LVENIAYDIRKTCLDGRGISRLSSSV*T<MAGSPCTT

Parental  CKCKNGSVCCSVDLECLHNN
          CKCK.G..CCSV.LEC.HNN
Retrocopy CKCKDGNACCSVNLECFHNN

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_1751 retrocopy.

TSS

Ailuropoda melanoleuca was not studied using FANTOM5 data.

Lab

retro_amel_1751 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 1 parental gene, and 1 retrocopy.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000014727	1 retrocopy	retro_amel_1751 ,