RetrogeneDB ID: retro_pvam_1043

Retrocopy location

• Organism: Megabat (Pteropus vampyrus)
• Coordinates: scaffold_245:277308..278120(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSPVAG00000016790
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: CBLL1
• Ensembl ID: ENSPVAG00000000781
• Aliases: None
• Description: Cbl proto-oncogene-like 1, E3 ubiquitin protein ligase [Source:HGNC Symbol;Acc:21225]

Sequence

>retro_pvam_1043
TTTGAAGATAACAAAGAAGGACAATATGACTGTAAAGGAAGTAAACTGTTGAGAAAAAAGAAAGAAAAAAACTCCTGAAT
ATTTTGGGAAGACTTTAAGGTAAACATCATAGGTAAAAAGGATGATTCAGTTCATTTCTGTGACAAATGTGATTTGCTCG
TTAAATCTATGGGTGAATGATTCTGTGCAAGCATCCTTTTTGTTATGACTGTGCTAATTTATATGAAAAAAAAATGGAAA
TAAGATGTGTAGCATAAGGCTGTAGTATTCCTGTGCTGTGAATTGAGCATACATGAGGTTATATTTTCATGTGTAGCACT
GTCCAAGGTTGCAAGAGAACGTATTTGTCTTAGAGAGACTTACAAGCTCATATTAATCACTGTCATAAGAGAGTTGAAAA
ACTTGTTACCTGTGCTCCACTGGAAAAAGTTCATCCTTTTACTGCCTTGCCAAACACTGAAACCCCTTAAATGCAGCTGG
CCAAGGACCATAAGAGGCATATTCCACCAGAGCAGGACACCTTGATGTCACCACCTCCCATGCAGCATGAGCCATACAAG
CACTATAATCAGCCACATGAGGGTCTTTGTGCTTCTCCAGTACAATTGTCTCCACCTCCATCTCCTTCAGTCCATCGGGA
AACCATTAGTATTGCAACAAGTGAATATAGAAATTTAATAATCATCCTTATTCAGGATGACTCTAATTCTGGTGCTAAGC
AACCATCATTTCCTGCTTTAGCACCCGCTCACCATCACATCGAATATCAAATTCAACCATCGATATTGCACTATTACTCT
ATTATGCTTCCA

Alignment

ORF - retro_pvam_1043 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 55.56 %
• Parental protein coverage: 56.01 %
• Number of stop codons detected: 7
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  FDYNEEERYDCKGGELFGNQRRFPGHLFW-DFQINIVGEKDDTPVHFCDKCGLPIK-IYGRMIPCKHVFC
          F..N.E..YDCKG..L...........FW.DF..NI.G.KDD..VHFCDKC.L..K.IYG.MI.CKH.FC
Retrocopy FEDNKEGQYDCKGSKLLXXXXXXXS*IFWEDFKVNIIGKKDDS-VHFCDKCDLLVK<IYG*MILCKHPFC

Parental  YDCAILHEKKGDKMCP--GCSDPVQRIEQCTRGSLFMCSIVQGCKRTYLSQRDLQAHINHRHMRAGKPVT
          YDCA.L........C...GCS.PV..IE..T.G..FMCS.VQGCKRTYLS.RDLQAHINH.H.R..K.VT
Retrocopy YDCANLYXXXXEIRCVA*GCSIPVL*IEH-T*GYIFMCSTVQGCKRTYLS*RDLQAHINHCHKRVEKLVT

Parental  RASLENVHPPIAPPPTEIPDRFIMPPDKHHMSHIPPKQHIMMPPPPLQHVPHEHYNQPHEDIRAPPAELS
          .A.LE.VHP..A.P.TE.P........K.H...IPP.Q...M.PPP.QH.P..HYNQPHE...A.P..LS
Retrocopy CAPLEKVHPFTALPNTETP*MQLAKDHKRH---IPPEQDTLMSPPPMQHEPYKHYNQPHEGLCASPVQLS

Parental  MAPPPPRSVSQETFRISTRKHSNLITVPIQDDSNSGAREPPPPAPAPAHHHPEYQGQPVVSHPHHIMPP
          ..PPP..SV..ET..I.T....NLI...IQDDSNSGA..P..PA.APAHHH.EYQ.QP...H...IM.P
Retrocopy --PPPSPSVHRETISIATSEYRNLIIILIQDDSNSGAKQPSFPALAPAHHHIEYQIQPSILHYYSIMLP

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_1043 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 3 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000031990	1 retrocopy	retro_cfam_2047,
Loxodonta africana	ENSLAFG00000029522	1 retrocopy	retro_lafr_711,
Pteropus vampyrus	ENSPVAG00000000781	1 retrocopy	retro_pvam_1043 ,