RetrogeneDB ID: retro_pvam_79

Retrocopy location

• Organism: Megabat (Pteropus vampyrus)
• Coordinates: GeneScaffold_1251:381718..382493(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: TSPAN5
• Ensembl ID: ENSPVAG00000003024
• Aliases: None
• Description: tetraspanin 5 [Source:HGNC Symbol;Acc:17753]

Sequence

>retro_pvam_79
CAGCACTTCCAGATCCCTGAGGTCTGCTGCTGTGAGAAACACTGTCTGTTGGGCTTCGACACTCTCTTCTGGGTGCTGGA
AGTCCCGTTCCTGGACTCAGCCTCTGGGCCTGGAGTAAGGGCATTCTCTCCACCATCTCGGCACTGACAGAACTGAGAGG
CCTTGTGAGGCTGTTTGTAGAGGTTGGAGGTGTCATGTCAGTGCTGGGTTTTGCCAGCTGCATCCAGGTTCCCCGAGAGA
ACATCTTCCTGCTCAAGTTCTTCTCCATGTTCCTCTGCCTCATCGTCTTCCTGGAGCTGGAGACTGGGATCCTAGCCTTC
GACTTCAAGGACTGAATTCGAGACCAGCTCAACCTCTTCATCAGCAAAGTCAAGGCCTATCGGGATGACATTGACCTCCA
GAACCTCTACTTTGCTTAGGAATTCTTGTCTTGCTGCTGAGCCTGAGGACCCAACAACTGGCACCTCAATAACTGTTTTG
ACTGCACTGACTTGAACCTGAGCTTGGAGCACTACGGGGTGCCCTTCTGCTGTGTCAGGGACCTTGTAGAAGATGTTCTC
AACACGCCGTGTGGCTACAATATCTGACACAAACTGAAGCTGGAGCAGAAAGCTCCATCCACACCAATAGCTGTGTGGGC
CAGCCTGAGAAGTGACTACAGGACAACTTGACCGTCGTGGCTAGGGTCTTTGTGGGCATCACCCTCCTCCTGATCTTTGG
CATCTGCCTAGCCCAGAACTTCATAAGTGACATTGGGGCAGTGAAGGCTAACTGG

Alignment

ORF - retro_pvam_79 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 56.93 %
• Parental protein coverage: 98.88 %
• Number of stop codons detected: 6
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  KHYKGPEVSCCIKYFIFGFNVIFWFLGITFL-GIGLWAWNEKGVLSNISSITDLGGFDPVWLFLVVGGVM
          .H...PEV.CC.K....GF...FW.L...FL.G..LWAW..KG.LS.IS..T.L.G...V.LF..VGGVM
Retrocopy QHFQIPEVCCCEKHCLLGFDTLFWVLEVPFL<GLSLWAWS-KGILSTISALTELRGL--VRLFVEVGGVM

Parental  FILGFAGCIGALRENTFLLKFFSVFLGIIFFLELTAGVLAFVFKDWIKDQLYFFINNNIRAYRDDIDLQN
          ..LGFA.CI...REN.FLLKFFS.FL..I.FLEL..G.LAF.FKD.I.DQL..FI.....AYRDDIDLQN
Retrocopy SVLGFASCIQVPRENIFLLKFFSMFLCLIVFLELETGILAFDFKD*IRDQLNLFI-SKVKAYRDDIDLQN

Parental  LIDFTQEYWQCCGAFGADDWNLNIYFNCTDSNASRERCGVPFSCCTKDPAEDVINTQCGYDARQKPEVDQ
          L..F..E...CC.A.G...W.LN..F.CTD.N.S.E..GVPF.CC..D..EDV.NT.CGY....K....Q
Retrocopy LY-FA*EFLSCC*A*GPNNWHLNNCFDCTDLNLSLEHYGVPF-CCVRDLVEDVLNTPCGYNI*HKLKLEQ

Parental  -QIVIYTKGCVPQFEKWLQDNLTIVAGIFIGIALLQIFGICLAQNLVSDIEAVRASW
          ....I.T..CV.Q.EK.LQDNLT.VA..F.GI.LL.IFGICLAQN..SDI.AV.A.W
Retrocopy <ESSIHTNSCVGQPEK*LQDNLTVVARVFVGITLLLIFGICLAQNFISDIGAVKANW

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_79 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 6 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000013851	1 retrocopy	retro_amel_742,
Canis familiaris	ENSCAFG00000010287	1 retrocopy	retro_cfam_314,
Choloepus hoffmanni	ENSCHOG00000013549	1 retrocopy	retro_chof_2337,
Dasypus novemcinctus	ENSDNOG00000012685	1 retrocopy	retro_dnov_91,
Echinops telfairi	ENSETEG00000007405	1 retrocopy	retro_etel_1985,
Pteropus vampyrus	ENSPVAG00000003024	1 retrocopy	retro_pvam_79 ,