RetrogeneDB ID: retro_pvam_872

Retrocopy location

• Organism: Megabat (Pteropus vampyrus)
• Coordinates: scaffold_14283:24925..25381(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: HMGB2
• Ensembl ID: ENSPVAG00000014656
• Aliases: None
• Description: high mobility group box 2 [Source:HGNC Symbol;Acc:5000]

Sequence

>retro_pvam_872
ATGAGTAAAGGAGACCCCAGCAAGCTGAGGGCAAGATGTCTTCGTATGCCTTCTCTGTGCAAACCTACCAGGAAGAGCAT
GAGAAGAAACACCCAGACTCTTCCATCAATTTTGCCAAATTCTCCAATACATGTTTGGAGTGATAGAAGATCATGTCTAC
AAAGGAAAAGTTCAAGTTCGAAGATATGGCAAAAAGTGACAAAGCTCGTTATTACAGGGAGATAAAAAATTATGCTCCTC
CCAAAGGTGATAAGAAAAGAAAGAAAAAAGATCCCAATGTTTCTAAAAGGGCTCTATCTGCCTTCTTCCTATTTTGCTCT
GAACATTGCCCAAAGATCAAAAGCGAGCACCTTGCTTATCCACTGGGGATACTGCAAAAAACTGGGTAAACCGTCAGCCA
AAGATAAGCAGTCATATGAACAGAAAGCAGCTAAGCTAAAGGGGAAATATGAGAAG

Alignment

ORF - retro_pvam_872 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 75.62 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 2
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  MGKGDPNKPR-GKMSSYAFFVQTCREEHKKKHPDSSVNFAEFSKKCSERWKTMSAKEKSKFEDMAKSDKA
          M.KGDP.K.R.GKMSSYAF.VQT..EEH.KKHPDSS.NFA.FS..C.E..K.MS.KEK.KFEDMAKSDKA
Retrocopy MSKGDPSKLR<GKMSSYAFSVQTYQEEHEKKHPDSSINFAKFSNTCLE**KIMSTKEKFKFEDMAKSDKA

Parental  RYDREMKNYVPPKGDKKGKKKDPNAPKRPPSAFFLFCSEHRPKIKSEH-PGLSIGDTA-KKLGEMWSEQS
          RY.RE.KNY.PPKGDKK.KKKDPN..KR..SAFFLFCSEH.PKIKSEH.P.LS.GDTA.KKLG......S
Retrocopy RYYREIKNYAPPKGDKKRKKKDPNVSKRALSAFFLFCSEHCPKIKSEH<PCLSTGDTA<KKLG----KPS

Parental  AKDKQPYEQKAAKLKEKYEK
          AKDKQ.YEQKAAKLK.KYEK
Retrocopy AKDKQSYEQKAAKLKGKYEK

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_872 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 13 parental genes, and 31 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000015101	1 retrocopy	retro_btau_58,
Dasypus novemcinctus	ENSDNOG00000019440	4 retrocopies	retro_dnov_1142, retro_dnov_1457, retro_dnov_454, retro_dnov_532,
Echinops telfairi	ENSETEG00000010379	3 retrocopies	retro_etel_1474, retro_etel_1841, retro_etel_2023,
Echinops telfairi	ENSETEG00000016379	1 retrocopy	retro_etel_414,
Felis catus	ENSFCAG00000004218	2 retrocopies	retro_fcat_279, retro_fcat_52,
Loxodonta africana	ENSLAFG00000010417	3 retrocopies	retro_lafr_1096, retro_lafr_1142, retro_lafr_595,
Macropus eugenii	ENSMEUG00000002256	3 retrocopies	retro_meug_1920, retro_meug_1989, retro_meug_550,
Monodelphis domestica	ENSMODG00000003527	3 retrocopies	retro_mdom_1160, retro_mdom_1919, retro_mdom_69,
Oryctolagus cuniculus	ENSOCUG00000000074	1 retrocopy	retro_ocun_1829,
Pteropus vampyrus	ENSPVAG00000000219	1 retrocopy	retro_pvam_356,
Pteropus vampyrus	ENSPVAG00000001431	6 retrocopies	retro_pvam_1156, retro_pvam_154, retro_pvam_429, retro_pvam_508, retro_pvam_774, retro_pvam_960,
Pteropus vampyrus	ENSPVAG00000014656	1 retrocopy	retro_pvam_872 ,
Rattus norvegicus	ENSRNOG00000013167	2 retrocopies	retro_rnor_173, retro_rnor_54,