RetrogeneDB ID: retro_pvam_358

Retrocopy location

• Organism: Megabat (Pteropus vampyrus)
• Coordinates: GeneScaffold_2718:192597..193049(-)
• Located in intron of: ENSPVAG00000005076

Retrocopy information

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

Parental gene information

• Parental gene symbol: UBE2N
• Ensembl ID: ENSPVAG00000013734
• Aliases: None
• Description: ubiquitin-conjugating enzyme E2N [Source:HGNC Symbol;Acc:12492]

Sequence

>retro_pvam_358
ATGGTCAGGCTTCCCCTCAGGACTACCAAGGAAACCCAGGGTATGCTAGCAGAACCAGTCCCCGACATCAAAGCAGAACC
AATGAGAGCCCATTATTTTCATGTGGTCATTACTGGCCCCCACGATCCTCCCCCTTTGAGGTAGGGATTTTAAAACTTGA
CCTATTCCTTCCAAAAGAATATCTGATGGCAGCCCTTAAAATACTTTTCATGACAAAAATTTATCATCCTAATGTAGACA
AACTGAGAAGAATATGTTTAGATATTTTGAAAGATAAGTGGTCCCCAGCACTGTAGATCTGCACAGTTCTGCTATTGATT
CAGGCTTTGTAAAGTGCTCCCAACCCAGATGATCCATTAGCAAATGATGTGGCAGAGCAGTGGAAGACCAACGAAGCCCA
AGCCATTGAAACAGTTAGAGCATGGCCCAGGCCGTAGGCCAGGAACAATATT

Alignment

ORF - retro_pvam_358 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 75.32 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MAGLPRRIIKETQRLLAEPVPGIKAEPDESNARYFHVVIAGPQDS-PFEGGTFK-LELFLPEEYPMAAPK
          M..LP.R..KETQ..LAEPVP.IKAEP....A.YFHVVI.GP.D..P..G..FK.L.LFLP.EY.MAA.K
Retrocopy MVRLPLRTTKETQGMLAEPVPDIKAEP--MRAHYFHVVITGPHDP>PL*GRDFK>LDLFLPKEYLMAALK

Parental  VRFMTKIYHPNVDKLGRICLDILKDKWSPALQIRTVLLSIQALLSAPNPDDPLANDVAEQWKTNEAQAIE
          ..FMTKIYHPNVDKL.RICLDILKDKWSPAL.I.TVLL.IQAL.SAPNPDDPLANDVAEQWKTNEAQAIE
Retrocopy ILFMTKIYHPNVDKLRRICLDILKDKWSPAL*ICTVLLLIQAL*SAPNPDDPLANDVAEQWKTNEAQAIE

Parental  TARAWTRLYAMNNI
          T.RAW.R..A.NNI
Retrocopy TVRAWPRP*ARNNI

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_358 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.

---

Parental genes homology:

Parental genes homology involve 11 parental genes, and 32 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000006177	1 retrocopy	retro_cfam_196,
Cavia porcellus	ENSCPOG00000008581	5 retrocopies	retro_cpor_1548, retro_cpor_230, retro_cpor_24, retro_cpor_655, retro_cpor_750,
Gorilla gorilla	ENSGGOG00000024332	4 retrocopies	retro_ggor_1079, retro_ggor_2140, retro_ggor_2720, retro_ggor_2969,
Loxodonta africana	ENSLAFG00000028985	1 retrocopy	retro_lafr_57,
Macropus eugenii	ENSMEUG00000002944	7 retrocopies	retro_meug_1236, retro_meug_1287, retro_meug_1453, retro_meug_1473, retro_meug_162, retro_meug_2009, retro_meug_31,
Macaca mulatta	ENSMMUG00000020634	3 retrocopies	retro_mmul_1587, retro_mmul_234, retro_mmul_72,
Monodelphis domestica	ENSMODG00000009451	2 retrocopies	retro_mdom_133, retro_mdom_1485,
Oryctolagus cuniculus	ENSOCUG00000011287	1 retrocopy	retro_ocun_100,
Pteropus vampyrus	ENSPVAG00000013734	2 retrocopies	retro_pvam_1420, retro_pvam_358 ,
Sarcophilus harrisii	ENSSHAG00000007776	1 retrocopy	retro_shar_105,
Tarsius syrichta	ENSTSYG00000008800	5 retrocopies	retro_tsyr_1476, retro_tsyr_1754, retro_tsyr_207, retro_tsyr_348, retro_tsyr_5,