RetrogeneDB ID: retro_pvam_1428

Retrocopy location

• Organism: Megabat (Pteropus vampyrus)
• Coordinates: scaffold_8376:68851..69679(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CALR
• Ensembl ID: ENSPVAG00000014715
• Aliases: None
• Description: calreticulin [Source:HGNC Symbol;Acc:1455]

Sequence

>retro_pvam_1428
ATACCACTGCTGCTCTGCCTTCCTTGCCTGGTTGCTGTGGAACCCTTTGTCTACTTCAAAGAACAGTTTCTGGACGGAGA
CAGGTGGCCTAACTGCTGGTTTGAATACAAAAGTAAGTCGGATTTTGGAAAATTTCTTCTCAGTGCCAGCAAGTTCTATG
GTGACTTGAACAAAGATAAAGGGCTGCAGACAAGCCAGGATGCCCACTTCTGTGCCCTGTCAGCCAGATTCAAGCCCTTC
AACAACAAGGACCAGACACTGATGGTGCAGTTCACTGTGAAACACGAGCAAAACATTGACTGTAGGGGTGAGAATGTGAA
GCTATTTCCAGACGGTTTGGAGCAGACAAATATGCATGGAGACTCCAAATACAATATCATGTTTGGCCCTAACATCTGTG
CTCTGGCACTAAGAAGATTCATGTCATCCTCAACAACAAGGGCAAGAATGTGCTGATCAATAAAGACATCTGTTGCAAGG
ATGATGAATTCACACACCTGTACACACTGATTGTGCGGCCCAATAACACCTAGAAGGTGAAGATTGACAACAGCCATGTA
GAGTCCTGCTCCCTGGAGGACAACTGGGACTTCCTGCCACTCAAGAAGATAAAGGAGCCTGATGCTTCAAAGCCAGAAGA
CTTGGGTAAGCAGACCAAGACTGACGACGCCACAGTCTCCAAACCTGAGGACTCAGACAAACTCGAGCACATCCCTGACC
CCAATGCTAAGAACCTGAGGACTGGATGAAGAGATAGATGGAAAGTGGGAACCACCAATCATTCAGAACTCGGAATACAA
GGGTGAGTGGAAGCCCTGCCAGATAGAC

Alignment

ORF - retro_pvam_1428 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 77.86 %
• Parental protein coverage: 66.43 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  VPLLLGLLGLAAAEPVVYFKEQFLDGDGWTNRWIESKHKSDFGKFVLSAGKFYGDLDKDKGLQTSQDARF
          .PLLL.L..L.A.EP.VYFKEQFLDGD.W.N.W.E.K.KSDFGKF.LSA.KFYGDL.KDKGLQTSQDA.F
Retrocopy IPLLLCLPCLVAVEPFVYFKEQFLDGDRWPNCWFEYKSKSDFGKFLLSASKFYGDLNKDKGLQTSQDAHF

Parental  YALSARFEPFSNKDQTLVVQFTVKHEQNIDCGGGYVKLFPDGLDQTDMHGDSEYNIMFGPDICG-PGTKK
          .ALSARF.PF.NKDQTL.VQFTVKHEQNIDC.G..VKLFPDGL.QT.MHGDS.YNIMFGP.IC...GTKK
Retrocopy CALSARFKPFNNKDQTLMVQFTVKHEQNIDCRGENVKLFPDGLEQTNMHGDSKYNIMFGPNICA<SGTKK

Parental  VHVIFNYKGKNVLINKDIRCKDDEFTHLYTLIVRPDNTYEVKIDNSQVESGSLEDDWDFLPPKKIKDPDA
          .HVI.N.KGKNVLINKDI.CKDDEFTHLYTLIVRP.NT..VKIDNS.VES.SLED.WDFLP.KKIK.PDA
Retrocopy IHVILNNKGKNVLINKDICCKDDEFTHLYTLIVRPNNT*KVKIDNSHVESCSLEDNWDFLPLKKIKEPDA

Parental  SKPEDWDERAKIDDPTDSKPEDWDKPEHIPDPDAK-KPEDW-DEEMDGEWEPPVIQNPEYKGEWKPRQID
          SKPED.....K.DD.T.SKPED.DK.EHIPDP.AK..PEDW.DEE.DG.WEPP.IQN.EYKGEWKP.QID
Retrocopy SKPEDLGKQTKTDDATVSKPEDSDKLEHIPDPNAK<EPEDW<DEEIDGKWEPPIIQNSEYKGEWKPCQID

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_1428 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 2 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Myotis lucifugus	ENSMLUG00000012776	1 retrocopy	retro_mluc_2433,
Pteropus vampyrus	ENSPVAG00000014715	2 retrocopies	retro_pvam_1071, retro_pvam_1428 ,