RetrogeneDB ID: retro_pvam_1071

Retrocopy location

• Organism: Megabat (Pteropus vampyrus)
• Coordinates: scaffold_2613:15298..16164(-)
• 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_1071
ATGCTCTTACCTGAGCTACTGCTGCTCGGCCTTCTCAGCCTGGCTGTCAAGGAACCCGTCTTCTATTTCAAGGAACAGTT
TCTGGACAGAGACAGGCTGATCAACTGCTGGACTGAATCCAAACACAAGTCGAATTTTGGAAAATATGTTCTCAGTGCCA
GCAAGTTCTACAATGAGTTGGACAAAGATAAAGGGCTGCAGACAAGCCAGGATGCCCACTTTCTATGCCCTGTCAGCCAG
ATTCGAGCACTTCAGCAACAAGGACCAGACGTTGGTGGTGCAGTTGACCGTGAAACATGAGCAGAACATCGACCATGGGG
GTGGCTACATAAAGCTATTTCCAGATGTTTTGGACCAGACGGATATGAAAGGAGACACTGAATACAGCATCATGTCTGGC
CCTGACATCTATGGCCCCAGCACCAAGAAGAGTCATGTCATCTTCAAGCACAAGGGCAAGAACGTGCTGATCAATAAGGA
CATCCATTGCAAGGATGATGAATTCACACACCTGACACATTGATTGTGTGACTGATAACACCTATGAGGTGAAGATTGAC
AGCAGTCAGGTGGAATCAGGCTCCCTGGAGAATGATTGGGACTTTCTGCCACCCAAGAAGATAAAGGTTCCTGATGTTTC
AAAGCCCAAAGACTGGGACAAGCAGGCCAACATTGATGACACCACAGACTCCAAACCTAAGGATGGGAACAAGTCCAAGC
ACAACCCTGACGCTGATGCTAAGAAGCCCAAGGACTGGGTTGAAGAGATGGATGGAGAGTGGGAACCACCAGTGATCTAA
GAACCTGAATACAAGGGCGAATGGAAGCCCTGGCAGATCGGCAACCCAGATTACAAGGGCAGTTGG

Alignment

ORF - retro_pvam_1071 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 78.77 %
• Parental protein coverage: 69.3 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  MLLPVPLLLGLLGLAAAEPVVYFKEQFLDGDGWTNRWIESKHKSDFGKFVLSAGKFYGDLDKDKGLQTSQ
          MLLP..LLLGLL.LA..EPV.YFKEQFLD.D...N.W.ESKHKS.FGK.VLSA.KFY..LDKDKGLQTSQ
Retrocopy MLLPELLLLGLLSLAVKEPVFYFKEQFLDRDRLINCWTESKHKSNFGKYVLSASKFYNELDKDKGLQTSQ

Parental  DARF-YALSARFEPFSNKDQTLVVQFTVKHEQNIDCGGGYVKLFPDGLDQTDMHGDSEYNIMFGPDICGP
          DA.F.YALSARFE.FSNKDQTLVVQ.TVKHEQNID.GGGY.KLFPD.LDQTDM.GD.EY.IM.GPDI.GP
Retrocopy DAHF>YALSARFEHFSNKDQTLVVQLTVKHEQNIDHGGGYIKLFPDVLDQTDMKGDTEYSIMSGPDIYGP

Parental  GTKKVHVIFNYKGKNVLINKDIRCKDDEFTHLY-TLIV-RPDNTYEVKIDNSQVESGSLEDDWDFLPPKK
          .TKK.HVIF..KGKNVLINKDI.CKDDEFTHL..TLIV...DNTYEVKID.SQVESGSLE.DWDFLPPKK
Retrocopy STKKSHVIFKHKGKNVLINKDIHCKDDEFTHLT<TLIV<VTDNTYEVKIDSSQVESGSLENDWDFLPPKK

Parental  IKDPDASKPEDWDERAKIDDPTDSKPEDWDKPEHIPDPDAKKPEDWDEEMDGEWEPPVIQNPEYKGEWKP
          IK.PD.SKP.DWD..A.IDD.TDSKP.D..K..H.PD.DAKKP.DW.EEMDGEWEPPVI..PEYKGEWKP
Retrocopy IKVPDVSKPKDWDKQANIDDTTDSKPKDGNKSKHNPDADAKKPKDWVEEMDGEWEPPVI*EPEYKGEWKP

Parental  RQIDNPDYKGTW
          .QI.NPDYKG.W
Retrocopy WQIGNPDYKGSW

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_1071 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,