RetrogeneDB ID: retro_pvam_288

Retrocopy location

• Organism: Megabat (Pteropus vampyrus)
• Coordinates: GeneScaffold_236:162881..163216(-)
• Located in intron of: ENSPVAG00000011653

Retrocopy information

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

Parental gene information

• Parental gene symbol: SOD2
• Ensembl ID: ENSPVAG00000005302
• Aliases: None
• Description: superoxide dismutase 2, mitochondrial [Source:HGNC Symbol;Acc:11180]

Sequence

>retro_pvam_288
ATCACTCTTACCATTTTATGGACAAACCTAAGTCCTAACAATAGTGGAAAACCCAAAGGGGAGTTTCTGTAAGGCAGCAA
ATGTTACTTTGTTTCCTTTGACTAAGTTGAGAAGTTGACAGCTATATCTGTTGGCTTTCAACATTCAGATTAGGGTGGGC
TTAATCTCATTAAGTAACAAGGACACTTTCACATTGCTGCCTATTCTAATAAGGATCCATTGCAAGAAACAATAGGTCTA
TTCCATTTGGGGGGATTGATGTATGGGCATATGCTTAATGCCTTTAGTATAAAAGTGTCAGATCTCATTATCTTAAACCT
GTTTGAGATGTAATC

Alignment

ORF - retro_pvam_288 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 54.39 %
• Parental protein coverage: 50.9 %
• Number of stop codons detected: 7
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  INHTIFWTNLSPNGGGEPKGELLEVIKRDFGSFAKFKEKLTTVSAGVQGSGWGWLGFNKEQGRLQIAACP
          I..TI.WTNLSPN..G.PKGE.L...K..F.SF....EKLT..S.G.Q.S..G.L...K.QG...IAA..
Retrocopy ITLTILWTNLSPNNSGKPKGEFL*GSKCYFVSF-D*VEKLTAISVGFQHSD*GGLNLIK*QGHFHIAAYS

Parental  NQDPLQGTTGL-IPLLGIDVWEHAYYLQYKNVRPDYLKAIWNVI
          N.DPLQ.T.GL.IP..GIDVW..A..L.YK.VR..YLK....VI
Retrocopy NKDPLQETIGL<IPFGGIDVWAYA*CL*YKSVRSHYLKPV*DVI

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_288 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 24 parental genes, and 28 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000015466	1 retrocopy	retro_amel_786,
Canis familiaris	ENSCAFG00000000671	1 retrocopy	retro_cfam_1795,
Choloepus hoffmanni	ENSCHOG00000003215	4 retrocopies	retro_chof_1952, retro_chof_1966, retro_chof_2620, retro_chof_937,
Callithrix jacchus	ENSCJAG00000011664	1 retrocopy	retro_cjac_3032,
Dasypus novemcinctus	ENSDNOG00000007907	1 retrocopy	retro_dnov_1653,
Equus caballus	ENSECAG00000011797	2 retrocopies	retro_ecab_70, retro_ecab_840,
Echinops telfairi	ENSETEG00000016400	1 retrocopy	retro_etel_731,
Felis catus	ENSFCAG00000002843	1 retrocopy	retro_fcat_1200,
Homo sapiens	ENSG00000112096	1 retrocopy	retro_hsap_430,
Gorilla gorilla	ENSGGOG00000008212	1 retrocopy	retro_ggor_419,
Myotis lucifugus	ENSMLUG00000012242	1 retrocopy	retro_mluc_528,
Monodelphis domestica	ENSMODG00000007521	1 retrocopy	retro_mdom_373,
Mustela putorius furo	ENSMPUG00000005045	1 retrocopy	retro_mputfur_1382,
Nomascus leucogenys	ENSNLEG00000011061	1 retrocopy	retro_nleu_1023,
Otolemur garnettii	ENSOGAG00000017100	1 retrocopy	retro_ogar_1123,
Pongo abelii	ENSPPYG00000017143	1 retrocopy	retro_pabe_292,
Pan troglodytes	ENSPTRG00000018757	1 retrocopy	retro_ptro_327,
Pteropus vampyrus	ENSPVAG00000005302	1 retrocopy	retro_pvam_288 ,
Rattus norvegicus	ENSRNOG00000019048	1 retrocopy	retro_rnor_2221,
Sarcophilus harrisii	ENSSHAG00000014795	1 retrocopy	retro_shar_210,
Ictidomys tridecemlineatus	ENSSTOG00000008738	1 retrocopy	retro_itri_1432,
Tupaia belangeri	ENSTBEG00000002100	1 retrocopy	retro_tbel_665,
Tarsius syrichta	ENSTSYG00000000457	1 retrocopy	retro_tsyr_183,
Tursiops truncatus	ENSTTRG00000014364	1 retrocopy	retro_ttru_265,