RetrogeneDB ID: retro_pvam_559

Retrocopy location

• Organism: Megabat (Pteropus vampyrus)
• Coordinates: GeneScaffold_3749:178934..179334(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SFT2D1
• Ensembl ID: ENSPVAG00000012673
• Aliases: None
• Description: SFT2 domain containing 1 [Source:HGNC Symbol;Acc:21102]

Sequence

>retro_pvam_559
ATGGAGAAGCTGTGGCAGGTCCTGAATGTCCAGGACAACAAGGAGCAAGGTCAACCTCGCAGGTCAATGCTTCGTCCCTG
AGTTTCGGCACCAGGCTGAGGAGGTTTGCCATCTGCTTGGTGAGCGCTGTTTTCTCCTCTATCCTTGGAACTGGATTGCT
GTGGCTTCCGGGAGACAGAAAGCTTTTTGCGGTGTTTTATACCCTTGGAAATAATTGCTGCCTTAGCCAGCACGTTCTTT
TTAATGTGACCCATGAAGTAAGCGAAGAAAATGTTTGAAACAACAAGATTGTTTGCAACGATCATTATGATTTTGTTTCA
TTTTCACCTTGCGTGCTGCTCTTTGGTGGCATAAGGGGCTGGCCTTATTATTCTGCATATTGCAGTTCTTGTCAATGACC

Alignment

ORF - retro_pvam_559 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 75.54 %
• Parental protein coverage: 85.53 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  MEKLRRVLSGQDDEEQGL-TSQVLDASSLSFSTRLRWFAICFVSGVLFSILGTGLLWLPGGLKLFAVFYT
          MEKL..VL..QD..EQG..TSQV..ASSLSF.TRLR.FAIC.VS.V..SILGTGLLWLPG..KLFAVFYT
Retrocopy MEKLWQVLNVQDNKEQGQ<TSQV-NASSLSFGTRLRRFAICLVSAVFSSILGTGLLWLPGDRKLFAVFYT

Parental  FGN-IAALASTCFLMGPMKQLKKMFETTRLLATIIMIL-CFVLTLCAALWWHKKGLALLFCILQFLSMT
          .GN.IAALAST.FLM.PMK..KKMFETTRL.AT.I....CF..TL.AALWWHK.GLALLFCILQFLSMT
Retrocopy LGN>IAALASTFFLM*PMK*AKKMFETTRLFAT-IIMI>CFIFTLRAALWWHK-GLALLFCILQFLSMT

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_559 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 11 parental genes, and 22 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000009311	3 retrocopies	retro_amel_1244, retro_amel_1452, retro_amel_374,
Bos taurus	ENSBTAG00000002993	5 retrocopies	retro_btau_1458, retro_btau_1460, retro_btau_31, retro_btau_546, retro_btau_900,
Canis familiaris	ENSCAFG00000000811	2 retrocopies	retro_cfam_283, retro_cfam_551,
Equus caballus	ENSECAG00000019479	1 retrocopy	retro_ecab_1029,
Mus musculus	ENSMUSG00000073468	1 retrocopy	retro_mmus_164,
Oryctolagus cuniculus	ENSOCUG00000001200	1 retrocopy	retro_ocun_1492,
Otolemur garnettii	ENSOGAG00000006302	1 retrocopy	retro_ogar_1601,
Ochotona princeps	ENSOPRG00000003408	2 retrocopies	retro_opri_37, retro_opri_809,
Pongo abelii	ENSPPYG00000017165	1 retrocopy	retro_pabe_181,
Pteropus vampyrus	ENSPVAG00000012673	3 retrocopies	retro_pvam_1340, retro_pvam_465, retro_pvam_559 ,
Tupaia belangeri	ENSTBEG00000000045	2 retrocopies	retro_tbel_3277, retro_tbel_747,