RetrogeneDB ID: retro_amel_1726

Retrocopy location

• Organism: Panda (Ailuropoda melanoleuca)
• Coordinates: GL194109.1:274999..275768(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: HNRNPA1
• Ensembl ID: ENSAMEG00000000717
• Aliases: None
• Description: None

Sequence

>retro_amel_1726
ATGTCTAAGTCAGAGTCTCCCAAAGAGCCTGAACAGCTGCGGAAGCTCTTCATTGGAGGTCTGAGCTTTGAAACAACTGA
TGAGAGTCTGAGGAGCCATTTTGAGCAATGGGGAACGCCTGCAGACTGTGTGATGATGAGAGATCCAAACACCAAGCGCT
CCAGAGGCTTTGGGTTTGTCACGTATGCCACTGTGGAGGAGGGGGGTGCAGCCACGAATGCAAGGCCACACAGCGTGGAT
GGAAGAGTTGTGGAACCAACGAGGGCTGCTCGAGAGAAGATTCTCAAAGACCTGGTGCCCATTTAACTGTGAAAAAGATT
TTTGTTGCTGGCATTAAAGAAGACAGTGAAGAACACCATCTAAGAGATTATTTTGAACAGTGTGGGAAAATTGAAGTGAT
TGAGATCATGACTGGCCGAGGCAGTGGCAAAAAGAGAGGTTTTGCTTTTGTAACATTTGATGACCACGACTCTGTAGACG
AGATAGTCGTTCAAAAATACCATACTGTGAATGGCCACAACTGTGAAGTAAGGAGAGCCCTATCTAAGCAAGAGATGGTG
AGTGCTTCATCCAGCCAAAGAGGTCGAAGTGGTTCTGGAAACTTCGGTGGTGGTCGTGGAGGTGGTTTTGGTGGGAATGA
CAATTTTGGTCGCGGAGGGGACTTCAGTGGGTGAGGTGGCTTTGGCGGCATTCGAGGTGGTGGTGGATATGGGGCAGTGG
GGATGGCTGTAACGGATTTGGTAATGATGGAAGCAACTTTGGAGGTGGC

Alignment

ORF - retro_amel_1726 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 89.96 %
• Parental protein coverage: 69.09 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MSKSESPKEPEQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDA
          MSKSESPKEPEQLRKLFIGGLSFETTDESLRSHFEQWGT..DCV.MRDPNTKRSRGFGFVTYATVEE..A
Retrocopy MSKSESPKEPEQLRKLFIGGLSFETTDESLRSHFEQWGTPADCVMMRDPNTKRSRGFGFVTYATVEEGGA

Parental  AMNARPHKVDGRVVEPKRAV-SREDSQRPGAHLTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTD
          A.NARPH.VDGRVVEP.RA..SREDSQRPGAHLTVKKIFV.GIKED.EEHHLRDYFEQ.GKIEVIEIMT.
Retrocopy ATNARPHSVDGRVVEPTRAA<SREDSQRPGAHLTVKKIFVAGIKEDSEEHHLRDYFEQCGKIEVIEIMTG

Parental  RGSGKKRGFAFVTFDDHDSVDKIVIQKYHTVNGHNCEVRKALSKQEMASASSSQRGRSGSGNFGGGRGGG
          RGSGKKRGFAFVTFDDHDSVD.IV.QKYHTVNGHNCEVR.ALSKQEM.SASSSQRGRSGSGNFGGGRGGG
Retrocopy RGSGKKRGFAFVTFDDHDSVDEIVVQKYHTVNGHNCEVRRALSKQEMVSASSSQRGRSGSGNFGGGRGGG

Parental  FGGNDNFGRGGNFSGRGGFGGSRGGGGYG-GSGDGYNGFGNDGGYGGGG
          FGGNDNFGRGG.FSG.GGFGG.RGGGGYG.GSGDG.NGFGNDG...GGG
Retrocopy FGGNDNFGRGGDFSG*GGFGGIRGGGGYG<GSGDGCNGFGNDGSNFGGG

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_1726 retrocopy.

TSS

Ailuropoda melanoleuca was not studied using FANTOM5 data.

Lab

retro_amel_1726 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 8 parental genes, and 22 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000000717	3 retrocopies	retro_amel_1726 , retro_amel_547, retro_amel_925,
Ailuropoda melanoleuca	ENSAMEG00000011920	4 retrocopies	retro_amel_1407, retro_amel_557, retro_amel_715, retro_amel_765,
Dasypus novemcinctus	ENSDNOG00000009228	7 retrocopies	retro_dnov_1059, retro_dnov_1670, retro_dnov_1944, retro_dnov_2081, retro_dnov_250, retro_dnov_320, retro_dnov_374,
Mustela putorius furo	ENSMPUG00000004620	1 retrocopy	retro_mputfur_34,
Mustela putorius furo	ENSMPUG00000005735	2 retrocopies	retro_mputfur_1378, retro_mputfur_653,
Oryctolagus cuniculus	ENSOCUG00000013350	1 retrocopy	retro_ocun_1675,
Otolemur garnettii	ENSOGAG00000029707	3 retrocopies	retro_ogar_1721, retro_ogar_205, retro_ogar_2321,
Oreochromis niloticus	ENSONIG00000012248	1 retrocopy	retro_onil_38,