RetrogeneDB ID: retro_pvam_936

Retrocopy location

• Organism: Megabat (Pteropus vampyrus)
• Coordinates: scaffold_17634:5185..6145(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSPVAG00000002533
• Aliases: None
• Description: None

Sequence

>retro_pvam_936
TTGGCGGGAGGCGAGGCTAGAGTGACTTTGGGGCAACCGCATTTTTCTCGCCAGGATCTTGCCAACTTGAATGTTACCAA
ATTTACCCCACTTTCACACGAAGTTATCAGCAGACAATCCACAATTAATATAGGTACAACTGGTCATGTAGCTCATGGGA
AACTCACAGTTATAAAAGCTATTTCTGGAGTTCACACTGTCAGGTCCAAAAATGAACTAGAGAGAAATATTGCAATCAAG
CTTGGATATGCTGATGTTAAGATTTATAAACTTGATGACCCAAGTTGTCCTCGGCCAGAATGTTATGAATCCTGTGGAAG
CATACACCTGATGAGTTTCCTACAGAGGTTCTGGGGACCAAAAGGAACTTCAAATTAGTCAAACATGTTTCCTTTGTTGA
CTGTCCTGGCCACGATATTTTGATGGCTACTATGCTGAACGGTGCAGCCGTGATGGATGCAGCTCTTCTGTTGATAGCTG
GTAATGAGTCTTGTCCTTAGCCTCAGACGTATGAACACCTGGCTGCTATAGAAATCATGAAACTGAAGCATATTTTGATT
CTATAAAATAAAATTGATTTGTAAAAGAAAGCCAGGCTAAAGAACAATGCGAACAGATCCTTGCATTTGTACAAGGTACA
GTAGCAGAAGTAGCTCCTATTATTCCAATGTCTGCTCAGCTGAAATACAATACTGAAGTTGTCTTTGAGTATATAGTAAA
GAAAATTCCAGTACCTCTAAGAGATTTTACTTCAGAACTCCAACTCATTGTTATTAGGTCCTTTGATGTCAACCAACCTG
GCTATGAAGTTGATGACCTTAAGGGGGTTGTAGCTGGTGGTAGTATTATAAAAGGAGTGTTAAAGGTGGGCTAGGAAATA
AAGTCAGACCTAGTATTTCCAAAGATAGTGAAGGAAAACTCATGTGTAAACCAATCTTTTCCAAAATTGTATCACTGTGG

Alignment

ORF - retro_pvam_936 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.54 %
• Parental protein coverage: 68.02 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  MAGGEAGVTLGQPHLSRQDLATLDVTKLTPLSHEVISRQATINIGTIGHVAHGKSTVVKAISGVHTV-FK
          .AGGEA.VTLGQPH.SRQDLA.L.VTK.TPLSHEVISRQ.TINIGT.GHVAHGK.TV.KAISGVHTV..K
Retrocopy LAGGEARVTLGQPHFSRQDLANLNVTKFTPLSHEVISRQSTINIGTTGHVAHGKLTVIKAISGVHTVRSK

Parental  NEL-RNITIKLGYANAKIYKLDDPCCPRPECYRSCGS-STPDEFPTDIPGTKGNF-LVKHVSFVDCPGHD
          NEL.RNI.IKLGYA..KIYKLDDP.CPRPECY.SCGS..TPDEFPT...GTK.NF.LVKHVSFVDCPGHD
Retrocopy NELERNIAIKLGYADVKIYKLDDPSCPRPECYESCGS<HTPDEFPTEVLGTKRNFKLVKHVSFVDCPGHD

Parental  ILMATMLNGAAVMDAALLLIAGNESCPQPQTSEHLAAIEIMKLKHILILQNKIDL-VKESQAKEQYEQIL
          ILMATMLNGAAVMDAALLLIAGNESCP.PQT.EHLAAIEIMKLKHILIL.NKIDL.VKESQAKEQ.EQIL
Retrocopy ILMATMLNGAAVMDAALLLIAGNESCP*PQTYEHLAAIEIMKLKHILIL*NKIDL<VKESQAKEQCEQIL

Parental  AFVQGTVAEGAPIIPISAQLKYNIEVVCEYIVKKIPVPPRDFTSEPRLIVIRSFDVNKPGCEVDDLKGGV
          AFVQGTVAE.APIIP.SAQLKYN.EVV.EYIVKKIPVP.RDFTSE..LIVIRSFDVN.PG.EVDDLKG.V
Retrocopy AFVQGTVAEVAPIIPMSAQLKYNTEVVFEYIVKKIPVPLRDFTSELQLIVIRSFDVNQPGYEVDDLKGVV

Parental  AGGSILKGVLKVGQEI-EVRPGIVSKDSEGKLMCKPIFSKIVSLF
          AGGSI.KGVLKVG.EI..VRP.I.SKDSEGKLMCKPIFSKIVSL.
Retrocopy AGGSIIKGVLKVG*EI<KVRPSI-SKDSEGKLMCKPIFSKIVSLW

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_936 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 11 parental genes, and 21 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000014337	1 retrocopy	retro_btau_1497,
Dasypus novemcinctus	ENSDNOG00000018584	1 retrocopy	retro_dnov_1454,
Equus caballus	ENSECAG00000017343	1 retrocopy	retro_ecab_810,
Echinops telfairi	ENSETEG00000000341	4 retrocopies	retro_etel_1061, retro_etel_126, retro_etel_1590, retro_etel_2017,
Loxodonta africana	ENSLAFG00000011052	1 retrocopy	retro_lafr_971,
Macaca mulatta	ENSMMUG00000006979	4 retrocopies	retro_mmul_1965, retro_mmul_2258, retro_mmul_473, retro_mmul_713,
Monodelphis domestica	ENSMODG00000007541	2 retrocopies	retro_mdom_1650, retro_mdom_732,
Pongo abelii	ENSPPYG00000020194	1 retrocopy	retro_pabe_10,
Pteropus vampyrus	ENSPVAG00000002533	1 retrocopy	retro_pvam_936 ,
Sus scrofa	ENSSSCG00000012178	1 retrocopy	retro_sscr_805,
Tursiops truncatus	ENSTTRG00000012474	4 retrocopies	retro_ttru_1080, retro_ttru_1638, retro_ttru_617, retro_ttru_686,