RetrogeneDB ID: retro_amel_792

Retrocopy location

• Organism: Panda (Ailuropoda melanoleuca)
• Coordinates: GL192640.1:742911..743462(+)
• Located in intron of: ENSAMEG00000008496

Retrocopy information

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

Parental gene information

• Parental gene symbol: CREG1
• Ensembl ID: ENSAMEG00000000024
• Aliases: None
• Description: None

Sequence

>retro_amel_792
GGCGCCAGGGGTGCTGCTGGTATCACCGGCACCGCCGTGCCACTGCCCCACAAGGACGCAGAGCACATGGCCCACTTCGT
GACATGCATCTGTGACTGGGGCGCACTGGCCACACTCTCCACGGAGGAGGCAGTGCATGGCTAGGCCTTCGTTGACGTCT
TCTCACTCAGCGACGGGCCCCCAGGCGTGGGCAGCAGCGTGCCCTGCTCCTGCCCGAGCCCACTGCTGCAGTTGGTGGGC
AACCCTCAGGAAAATCCACATGCTACACCAGCCGCGTCTTTGGCATAGACTGACTTCTGCAGGAAGCAAGTATTTGATCC
CCACGGTCCCCTCTCTGCTCACATAATGCTGTCAGGAACTGTTACTAATGTGAATGAAATGGAAATGGACTTTGCCAGGC
ATTCACTGTTCATCCAGCACCCTGACATGAAAACCTGGCCTTCCAGCCATAATTGGTTCTTTGCTAAGTTGAATTTAACC
AACATCTGGATCCTGGACCACTTTGGTGGACCAAAAATAGTGATACCTGAAAATACTATAATGTCACATTT

Alignment

ORF - retro_amel_792 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 63.78 %
• Parental protein coverage: 99.44 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  GLRTVAGVTVMAARA--RGSARVARFVTHVCDWGALATLSTEPAVRG----SILSLSDGPPGAGSGVPYF
          G.R..AG.T..A...........A.FVT..CDWGALATLSTE.AV.G.......SLSDGPPG.GS.VP..
Retrocopy GARGAAGITGTAVPLPHKDAEHMAHFVTCICDWGALATLSTEEAVHG*AFVDVFSLSDGPPGVGSSVPCS

Parental  YLSPMQQSVGNLQENPHASLTMSLAQTNFCRKQGFDPQSPLCAHIILSGTVTKVNQTEMGFAKQSLFVRH
          ..SP..Q.VGN.QENPHA....SLA.T.FCRKQ.FDP..PL.AHI.LSGTVT.VN..EM.FA..SLF..H
Retrocopy CPSPLLQLVGNPQENPHATPAASLA*TDFCRKQVFDPHGPLSAHIMLSGTVTNVNEMEMDFARHSLFIQH

Parental  PEMKTWPSSHNWFFAKLNISNIWVVDYFGGPKIVTPE-EYYNVTF
          P.MKTWPSSHNWFFAKLN..NIW..D.FGGPKIV.PE..YYNVTF
Retrocopy PDMKTWPSSHNWFFAKLNLTNIWILDHFGGPKIVIPE<KYYNVTF

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_792 retrocopy.

TSS

Ailuropoda melanoleuca was not studied using FANTOM5 data.

Lab

retro_amel_792 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	ENSAMEG00000000024	1 retrocopy	retro_amel_792 ,
Canis familiaris	ENSCAFG00000015414	1 retrocopy	retro_cfam_963,
Monodelphis domestica	ENSMODG00000027768	1 retrocopy	retro_mdom_1918,