RetrogeneDB ID: retro_pvam_448

Retrocopy location

• Organism: Megabat (Pteropus vampyrus)
• Coordinates: GeneScaffold_3196:2274..3047(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SEPT2
• Ensembl ID: ENSPVAG00000000558
• Aliases: None
• Description: septin 2 [Source:HGNC Symbol;Acc:7729]

Sequence

>retro_pvam_448
GAGAAAATGGAAAGAACTGCCCAAATTTAGGCCTCTATGTTGAGATTGAAGAGCGAGTGGTCAAGCTGCGCCTGACGGTG
GTGGACACCCCCGACTACAATGATGCCATCAACTGCAGGAATTGTTTTAAGACAATCATCTCCTACATCGACGAGCAGTT
TGAACGGTATCTGCACGACGAGAGTGGTCTGACTAGGCGGCACATCGTCGACGACAGGGTGCACTGCTGCTTTTACTTCA
TCTCGCCCTTTGGACACGGACTTAAGCCCTTAGATGTCGCGTTTATGAAGGCGATACACAACAAGGTCAATATTGTGCCT
GTCATCGCAAAAGCCTACACACTCACTCTGAAGGAACGCGAGCGCCTGAAGAAGAGGACTCTGGATGAAATCGAAGAACA
TAACATCAGCATCTATCACTTACCTGATGCAGAATCGGATGAAGACAAAGATTTTAAAGAGCAGACTAGGCTCCGCAAGG
CCAGTATCTCATTCTCCGTGGTTGGATCCAATCAGCTGATTGAAGCCAAAGGCAAGAAGGTCAGAGGCCGCCTCTACCCG
TGGGGTGTCGCCGAGGTGGAGAACCCGGAGCACAACGACTTTCTGAAGCTGAGGACAACGCTCATCGCTCACATTCAGGA
CCTCCGGGAAGTAACCCAGGACCTTCCCGATGAGAACTTCCGTTCTGAGAGGCTCAAAAGAGGCGGCAGAAAAGTAGAAA
ATGAGGACATGAATAAAGACCAAATTTTGGCAGGAAAGGAAGCTGAGCTCCGC

Alignment

ORF - retro_pvam_448 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 89.19 %
• Parental protein coverage: 69.73 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  EKIERTVQIEAST-VEIEERGVKLRLTVVDTPGYGDAINCRDCFKTIISYVDEQFERYLHDESGLNRRHI
          EK.ERT.QI.AS..VEIEER.VKLRLTVVDTP.Y.DAINCR.CFKTIISY.DEQFERYLHDESGL.RRHI
Retrocopy EKMERTAQI*ASM<VEIEERVVKLRLTVVDTPDYNDAINCRNCFKTIISYIDEQFERYLHDESGLTRRHI

Parental  IDNRVHCCFYFISPFGHGLKPLDVAFMKAIHNKVNIVPVIAKADTLTLKERERLKKRILDEIEEHNIKIY
          .D.RVHCCFYFISPFGHGLKPLDVAFMKAIHNKVNIVPVIAKA.TLTLKERERLKKR.LDEIEEHNI.IY
Retrocopy VDDRVHCCFYFISPFGHGLKPLDVAFMKAIHNKVNIVPVIAKAYTLTLKERERLKKRTLDEIEEHNISIY

Parental  HLPDAESDEDEDFKEQTRLLKASIPFSVVGSNQLIEAKGKKVRGRLYPWGVVEVENPEHNDFLKLRTMLI
          HLPDAESDED.DFKEQTRL.KASI.FSVVGSNQLIEAKGKKVRGRLYPWGV.EVENPEHNDFLKLRT.LI
Retrocopy HLPDAESDEDKDFKEQTRLRKASISFSVVGSNQLIEAKGKKVRGRLYPWGVAEVENPEHNDFLKLRTTLI

Parental  THMQDLQEVTQDLHYENFRSERLKRGGRKVENEDMNKDQILLEKEAELR
          .H.QDL.EVTQDL..ENFRSERLKRGGRKVENEDMNKDQIL..KEAELR
Retrocopy AHIQDLREVTQDLPDENFRSERLKRGGRKVENEDMNKDQILAGKEAELR

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_448 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 16 parental genes, and 20 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000002608	1 retrocopy	retro_btau_1185,
Canis familiaris	ENSCAFG00000012960	1 retrocopy	retro_cfam_1477,
Choloepus hoffmanni	ENSCHOG00000008715	5 retrocopies	retro_chof_1371, retro_chof_1579, retro_chof_2198, retro_chof_275, retro_chof_614,
Callithrix jacchus	ENSCJAG00000006122	1 retrocopy	retro_cjac_1501,
Cavia porcellus	ENSCPOG00000013687	1 retrocopy	retro_cpor_845,
Loxodonta africana	ENSLAFG00000011964	1 retrocopy	retro_lafr_4,
Macropus eugenii	ENSMEUG00000016519	1 retrocopy	retro_meug_39,
Myotis lucifugus	ENSMLUG00000007108	1 retrocopy	retro_mluc_1594,
Monodelphis domestica	ENSMODG00000016041	1 retrocopy	retro_mdom_888,
Mustela putorius furo	ENSMPUG00000000166	1 retrocopy	retro_mputfur_436,
Nomascus leucogenys	ENSNLEG00000013873	1 retrocopy	retro_nleu_1848,
Otolemur garnettii	ENSOGAG00000004457	1 retrocopy	retro_ogar_2239,
Pteropus vampyrus	ENSPVAG00000000558	1 retrocopy	retro_pvam_448 ,
Rattus norvegicus	ENSRNOG00000017952	1 retrocopy	retro_rnor_1110,
Ictidomys tridecemlineatus	ENSSTOG00000013357	1 retrocopy	retro_itri_1227,
Drosophila melanogaster	FBgn0011710	1 retrocopy	retro_dmel_35,