RetrogeneDB ID: retro_amel_1637

Retrocopy location

• Organism: Panda (Ailuropoda melanoleuca)
• Coordinates: GL193817.1:341268..341523(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: HMGA1
• Ensembl ID: ENSAMEG00000001061
• Aliases: None
• Description: None

Sequence

>retro_amel_1637
CAGAGAAGCAGGGGCAGGGCGGGCCGCTCAAGCAGCTGGGTCCCCCGGATGGTGCTGGTAGGGGCCGGGGAACCCAGTGA
AGTGCCAACACCAAAGACACCTCGTGCCCGCCAAAGGGGAACAAAAAACAAGAGTGCTGCTAAGACTGGGAACACTGCCA
CGGCTCCAGGGAGGAAACCCAGGAGCAAACCCCCCAAAAAACTGGAGAAGGAGGAAGAAGAGGGGATCTTGCAGGAGTCC
CCAGAGGAGGCGCAG

Alignment

ORF - retro_amel_1637 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 62.79 %
• Parental protein coverage: 81.73 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  KRGRGRPRKQPPVSPGTALVGSQKEPSEVPTPKRPRGRPKGSKNKGAAKTRKTTTTPGRKPRGR-PKKLE
          .R.RGR........P...LVG...EPSEVPTPK.PR.R..G.KNK.AAKT..T.T.PGRKPR...PKKLE
Retrocopy QRSRGRAGRSSSWVPRMVLVGAG-EPSEVPTPKTPRARQRGTKNKSAAKTGNTATAPGRKPRSKPPKKLE

Parental  KEEEEGISQESSEEEQ
          KEEEEGI.QES.EE.Q
Retrocopy KEEEEGILQESPEEAQ

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_1637 retrocopy.

TSS

Ailuropoda melanoleuca was not studied using FANTOM5 data.

Lab

retro_amel_1637 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.

---

Parental genes homology:

Parental genes homology involve 10 parental genes, and 24 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000001061	1 retrocopy	retro_amel_1637 ,
Callithrix jacchus	ENSCJAG00000015226	2 retrocopies	retro_cjac_1197, retro_cjac_3158,
Homo sapiens	ENSG00000137309	4 retrocopies	retro_hsap_1175, retro_hsap_2277, retro_hsap_4663, retro_hsap_695,
Myotis lucifugus	ENSMLUG00000010085	2 retrocopies	retro_mluc_1619, retro_mluc_2429,
Macaca mulatta	ENSMMUG00000019529	2 retrocopies	retro_mmul_1276, retro_mmul_2406,
Mus musculus	ENSMUSG00000046711	1 retrocopy	retro_mmus_188,
Nomascus leucogenys	ENSNLEG00000008303	1 retrocopy	retro_nleu_1097,
Pongo abelii	ENSPPYG00000029838	4 retrocopies	retro_pabe_1941, retro_pabe_2441, retro_pabe_3623, retro_pabe_960,
Pan troglodytes	ENSPTRG00000040884	6 retrocopies	retro_ptro_1611, retro_ptro_2053, retro_ptro_3098, retro_ptro_499, retro_ptro_789, retro_ptro_807,
Rattus norvegicus	ENSRNOG00000000488	1 retrocopy	retro_rnor_164,