RetrogeneDB ID: retro_pvam_116

Retrocopy location

• Organism: Megabat (Pteropus vampyrus)
• Coordinates: GeneScaffold_1470:25320..25668(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: HMGA1
• Ensembl ID: ENSPVAG00000014283
• Aliases: None
• Description: high mobility group AT-hook 1 [Source:HGNC Symbol;Acc:5010]

Sequence

>retro_pvam_116
TCGAGCTCCAATTCCAGCCAACGCTTGGCCTCCAAGCAAAAAAGGACGGCACTGAGAAGCCAGGGCGGGGCAGGCCTCGC
AAGCCGCCTCGGGGGAGTCCTGGGGCGGCGCTGATAGGGAGTCGGAGAAAGCCCAGTGAAGTGCCAACACCGCAGAGACC
TCGGGCGACCCAAAGAGAGAAAAAACAACAGCGCTGCCAAGCCCAAAAACTAGAGGAGGAAGAAGAGGGCATCCCGCAGG
AGTCCTTAGAGGAGCAGTGACCGCGCAGTGCCACCTCACTGGGGGGCAGTTTCCTTCTGGAACTGGACGGCTCGGCTCCC
ACGGCCCCCGCCCCTTCCCATAGGCCCA

Alignment

ORF - retro_pvam_116 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 53.39 %
• Parental protein coverage: 65.48 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  SSSKSSQPLASKQE-KDGTEKRGRGRPRKQPPVSPGTTLVGSQKEPSEVPTPKRPRGRPKGSK-NKGRRR
          SSS.SSQ.LASKQ..KDGTEK.GRGRPRK.P..SPG..L.GS...PSEVPTP.RPR......K.N.....
Retrocopy SSSNSSQRLASKQK<KDGTEKPGRGRPRKPPRGSPGAALIGSRRKPSEVPTPQRPRATQREKK>NSAAKP

Parental  KK-RASRRSPQR---RSSDRAVPP--ASSSRSSFLLGLDAPLPLPPCP
          K..R...R...R...RSSDRAVPP.....S.......L..P.PLP..P
Retrocopy KN*RRKKRASRRSP*RSSDRAVPPHWGAVSFWNWTARLPRPPPLPIGP

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Pteropus vampyrus was not studied using RNA-Seq expression data.

ChIP-Seq

Pteropus vampyrus was not studied using ChIP-Seq data.

EST

Pteropus vampyrus was not studied using EST data.

TSS

Pteropus vampyrus was not studied using FANTOM5 data.

Lab

retro_pvam_116 was not experimentally validated.

Homology

Retrocopy orthology:

Pteropus vampyrus 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 7 parental genes, and 12 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000015226	2 retrocopies	retro_cjac_1197, retro_cjac_3158,
Macaca mulatta	ENSMMUG00000019529	2 retrocopies	retro_mmul_1276, retro_mmul_2406,
Mus musculus	ENSMUSG00000046711	1 retrocopy	retro_mmus_188,
Procavia capensis	ENSPCAG00000016076	1 retrocopy	retro_pcap_236,
Pongo abelii	ENSPPYG00000029838	4 retrocopies	retro_pabe_1941, retro_pabe_2441, retro_pabe_3623, retro_pabe_960,
Pteropus vampyrus	ENSPVAG00000014283	1 retrocopy	retro_pvam_116 ,
Rattus norvegicus	ENSRNOG00000000488	1 retrocopy	retro_rnor_164,