RetrogeneDB ID: retro_pvam_48

Retrocopy location

• Organism: Megabat (Pteropus vampyrus)
• Coordinates: GeneScaffold_1148:39785..40060(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RPL37A
• Ensembl ID: ENSPVAG00000006102
• Aliases: None
• Description: ribosomal protein L37a [Source:HGNC Symbol;Acc:10348]

Sequence

>retro_pvam_48
GCTGAACACACCAAGAGGGTTTAAATCATCAGCAAATTCGGGACTCGTTATGGTACCTCGCTCAGGAAAATGGTGAAGAA
GATTAAAATTGGCTGGCATGCCAAGTACACTCGCTCCTTCTGTGGCAAAACCAAAATGAAGAGACGAGCTGTGGGGCTCT
GCCACTGGGGTTCCTGCGTGGAGCAGCAGCTGGTGGTGCCTGGACCGACAACAGCACCACTTCTGCCAGCACAGTGAAGT
CAGGCACCAGGTGACTGAAGGAACTGAGAGACCAG

Alignment

ORF - retro_pvam_48 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 70.97 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  AKRTKKVGIVGKYGTRYGASLRKMVKKIEISQHAKYTCSFCGKTKMKRRAVGIWHCGSCMK-TVAGGAWT
          A..TK.V.I..K.GTRYG.SLRKMVKKI.I..HAKYT.SFCGKTKMKRRAVG..H.GSC.....AGGAWT
Retrocopy AEHTKRV*IISKFGTRYGTSLRKMVKKIKIGWHAKYTRSFCGKTKMKRRAVGLCHWGSCVE<AAAGGAWT

Parental  YN-TTSAVTVKSAIRRLKELKDQ
          .N.TTSA.TVKS..R.LKEL.DQ
Retrocopy DNSTTSASTVKSGTR*LKELRDQ

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_48 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 69 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000003377	24 retrocopies	retro_amel_109, retro_amel_1170, retro_amel_1197, retro_amel_1204, retro_amel_1248, retro_amel_1310, retro_amel_1349, retro_amel_1534, retro_amel_1597, retro_amel_1724, retro_amel_1815, retro_amel_1910, retro_amel_1929, retro_amel_248, retro_amel_424, retro_amel_428, retro_amel_475, retro_amel_482, retro_amel_606, retro_amel_737, retro_amel_809, retro_amel_83, retro_amel_920, retro_amel_942,
Latimeria chalumnae	ENSLACG00000011578	1 retrocopy	retro_lcha_71,
Loxodonta africana	ENSLAFG00000006849	5 retrocopies	retro_lafr_1010, retro_lafr_1015, retro_lafr_109, retro_lafr_987, retro_lafr_991,
Macropus eugenii	ENSMEUG00000004680	23 retrocopies	retro_meug_1094, retro_meug_111, retro_meug_1120, retro_meug_1289, retro_meug_1302, retro_meug_1399, retro_meug_1600, retro_meug_1705, retro_meug_2021, retro_meug_2061, retro_meug_2143, retro_meug_2173, retro_meug_24, retro_meug_290, retro_meug_458, retro_meug_463, retro_meug_496, retro_meug_502, retro_meug_571, retro_meug_691, retro_meug_813, retro_meug_814, retro_meug_83,
Otolemur garnettii	ENSOGAG00000000817	3 retrocopies	retro_ogar_1317, retro_ogar_3003, retro_ogar_69,
Petromyzon marinus	ENSPMAG00000000001	1 retrocopy	retro_pmar_11,
Pteropus vampyrus	ENSPVAG00000006102	12 retrocopies	retro_pvam_1074, retro_pvam_1346, retro_pvam_169, retro_pvam_204, retro_pvam_343, retro_pvam_48 , retro_pvam_652, retro_pvam_658, retro_pvam_669, retro_pvam_761, retro_pvam_765, retro_pvam_90,