RetrogeneDB ID: retro_pvam_1018

Retrocopy location

• Organism: Megabat (Pteropus vampyrus)
• Coordinates: scaffold_2281:169049..169784(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: TPRG1L
• Ensembl ID: ENSPVAG00000015273
• Aliases: None
• Description: tumor protein p63 regulated 1-like [Source:HGNC Symbol;Acc:27007]

Sequence

>retro_pvam_1018
GCAGCAACTGCGTCTGTGTGGTGTCAGGGTCCCAAGTCGGGCTGGGCAGGTGGAGTGGCCATGCAACAGCCACCGTGGCC
ACTCAGCATCCACGACCCCAAGCGCCCCGCGCGCGACAAGAACTTCGTGTTCCAGCCTCAAACCATCAAGTGGGCGGAGA
ACGAGGCCCACGTGATGGTCCTGCAGGTGGAGGACAATGACATCCAGGGGGTGTGGTACTGACGTAGGTGGTTTACTGGA
TTGACAATCAAAAGCGACTGGTGCTCGGAACCGACCGGGTGCTGCTCATCTGCAAACAGGACTTCATCAGCCTCCAGTGC
CGGATCACCTTAAATGAGGTGGACAGCATCTCCTACAGAGAATTCCAGTTTTCCCTGAAATCGCACAACAAGCAAGAAGG
TTTGGGGATTCACATTCAGTGGGATAAGCAGAGCTGCCCTTCCTTCATAAACGAATGGAATCCTTGGTCTGCCAACCAGC
TCTAGGCCAAGTTCATCCAGCACCTGATGGCCAGTGCTAACGAGAAGACCACTTCTATGTGCCAACTGGAAAGCTTCAAA
GCTCTGCTAATACAAGCTATCAAAAAAGGCCCAATAGAGAGTTCTTTGACAGGACAAGCCAACAGCATGCTGGTCTTAGA
GCAGCCCTCTTCATCAAGACCTACATGGGTTGATGTTCTTCATTAACCACGAGGCTAAATCGGGCTATTCCATGACCACT
GGCAAGATAGATTTC

Alignment

ORF - retro_pvam_1018 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 60.63 %
• Parental protein coverage: 92.96 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  AAGEEVGAGGGAGGGRPGTPLRQTLWPLSVHDPTRRARVKEYFVFRPGTIEQAVDEIRVVVRPVEDGDVQ
          AA...V...G...G...G....Q..WPLS.HDP.R.AR.K..FVF.P.TI..A..E..V.V..VED.D.Q
Retrocopy AATASVWCQGPKSGWAGGVAMQQPPWPLSIHDPKRPARDKN-FVFQPQTIKWAENEAHVMVLQVEDNDIQ

Parental  GVW-LLTEVDHWNNEKERLVLITDQSLLICKYDFISLQCQQVVRVALNAVDTISCGEFQFPPKSLNKREG
          GVW..LT.V..W.....RLVL.TD..LLICK.DFISLQC....R..LN.VD.IS..EFQF..KS.NK.EG
Retrocopy GVW<VLT*VVYWIDNQKRLVLGTDRVLLICKQDFISLQC----RITLNEVDSISYREFQFSLKSHNKQEG

Parental  LGIRIQWDKQSRPSFINRWNPWSTNVPYATFMEHPMAGADEKTASLCQLESFKALLIQAVKKAQKEHPLP
          LGI.IQWDKQS.PSFIN.WNPWS.N...A.F..H.MA.A.EKT.S.CQLESFKALLIQA.KK...E..L.
Retrocopy LGIHIQWDKQSCPSFINEWNPWSANQL*AKFIQHLMASANEKTTSMCQLESFKALLIQAIKKGPIESSLT

Parental  GQASGVLVLEQP-LLIETYV-GLMSFINNEAKLGYSMTRGKIGF
          GQA...LVLEQP.L.I.TY..GLM.FIN.EAK.GYSMT.GKI.F
Retrocopy GQANSMLVLEQP<LFIKTYM<GLMFFINHEAKSGYSMTTGKIDF

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_1018 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 4 parental genes, and 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Monodelphis domestica	ENSMODG00000006651	1 retrocopy	retro_mdom_1017,
Pteropus vampyrus	ENSPVAG00000015273	1 retrocopy	retro_pvam_1018 ,
Ictidomys tridecemlineatus	ENSSTOG00000007466	1 retrocopy	retro_itri_28,
Tupaia belangeri	ENSTBEG00000011399	7 retrocopies	retro_tbel_1982, retro_tbel_2169, retro_tbel_2300, retro_tbel_2302, retro_tbel_2339, retro_tbel_2599, retro_tbel_2603,