RetrogeneDB ID: retro_pvam_1267

Retrocopy location

• Organism: Megabat (Pteropus vampyrus)
• Coordinates: scaffold_5226:36696..37673(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: DDX5
• Ensembl ID: ENSPVAG00000001932
• Aliases: None
• Description: DEAD (Asp-Glu-Ala-Asp) box helicase 5 [Source:HGNC Symbol;Acc:2746]

Sequence

>retro_pvam_1267
TCAGGCTATTGGAATGACTGAGACTGCGGCAGGGATGGAGGGTTTGGTGCAACTCTATTTGGAGAAAGTAGAGCAGGGTC
ACTATCAGGAAAGAAGTTCGGAAACCCTGGGGAGAAATTAGTTAAAAAGAAGTGGAATCTTGATGAGTTACCCAAATTTG
AGAAGAATTTTTTATCAAGAACACCATGATTTGGCTAGGCACACAGCACAAGAGGTGGAAACATACAGAAAAATTAAGGA
AATTACAGTTAGATGTCATAACCGCCCAAAGCTAGGTCCGAATTTTTATGAAGCAAACTTCTCTGCAAATGTCATGGATG
TGATTGCAAGATAGAACTTTACTGAACCCACTGCTATTCAAGCTCAGGGATGGCCAGTTGCTCTAAGTGGATTGGATATG
GTTGGAATAGCACAGATTGGATTTGGGAAAACATTGTCTTATTTTCTGCCTTCCATTGTCCACATCAATCATCAGCCATT
CTTAGAGTGAGGTACTGGGCCTATTTGCTTGGTGCTGGCACCATGTTGGGAACAACACGTGCAGCAAGTAGCTGCTGAAT
ACTGTAGAACATGACAGTTGAAGTCTACTTGTATCTATGGCGGTGCTCCCAAGGGACCACAAATAATATGATTTGGAGAG
AGGTGTGGAAATCTATATCGCAATACCTTAAAGACTGGCTGACTTTTTAGAGTGTGGGTAAACAAATCGTAGAAGAACCA
CCTACCTTGTCTTTGATGAAGCAGATAGAATGTTTGATATGGGCTTCGAACCCCAAATAAGAAAGATTCTGGATGAAATA
AGTCATGACAGGCAAACTCTAATGTGGAGTGTGAATTGGCCAAAAGAAGTAAGACAGCTTGCTGAAGATTTCTTGAAAGA
CTAAATTTATATAAACATTGGCGCACTAAAACTGAGTGCAAACCACAACATTCTTTAGATTGTGGATGTGTGTGATGATG
TAGAAAAGGTTGAAAAA

Alignment

ORF - retro_pvam_1267 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 82.32 %
• Parental protein coverage: 53.18 %
• Number of stop codons detected: 8
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  SGYSSDRDRGRDRGFGAPRFGGSRAGPLSGKKFGNPGEKLVKKKWNLDELPKFEKNF-YQEHPDLARRTA
          SGY..D.D.GRD.GFGA..FG.SRAG.LSGKKFGNPGEKLVKKKWNLDELPKFEKNF.YQEH.DLAR.TA
Retrocopy SGYWND*DCGRDGGFGATLFGESRAGSLSGKKFGNPGEKLVKKKWNLDELPKFEKNF>YQEHHDLARHTA

Parental  QEVETYRRSKEITVRGHNCPKPVLNFYEANFPANVMDVIARQNFTEPTAIQAQGWPVALSGLDMVGVAQT
          QEVETYR..KEITVR.HN.PK...NFYEANF.ANVMDVIAR.NFTEPTAIQAQGWPVALSGLDMVG.AQ.
Retrocopy QEVETYRKIKEITVRCHNRPKLGPNFYEANFSANVMDVIAR*NFTEPTAIQAQGWPVALSGLDMVGIAQI

Parental  GSGKTLSYLLPAIVHINHQPFLERGDGPICLVLAPTRELAHVQQVAAEYCRACRLKSTSIYGGAPKGPQI
          G.GKTLSY.LP.IVHINHQPFLE.G.GPICLVLAP..E..HVQQVAAEYCR...LKST.IYGGAPKGPQI
Retrocopy GFGKTLSYFLPSIVHINHQPFLE*GTGPICLVLAPCWE-QHVQQVAAEYCRT*QLKSTCIYGGAPKGPQI

Parental  -RDLERGVEICIATPGRLIDFLECGKTNLRRTTYLVLDEADRMLDMGFEPQIRKIVDQIRPDRQTLMWSA
          ..DLERGVEI.IA.P.RL.DFLECG.TN.RRTTYLV.DEADRM.DMGFEPQIRKI.D.I..DRQTLMWS.
Retrocopy >YDLERGVEIYIAIP*RLADFLECG*TNRRRTTYLVFDEADRMFDMGFEPQIRKILDEISHDRQTLMWSV

Parental  TWPKEVRQLAEDFLKDYIHINIGALELSANHNILQIVDVCHDVEKDEK
          .WPKEVRQLAEDFLKD.I.INIGAL.LSANHNIL.IVDVC.DVEK.EK
Retrocopy NWPKEVRQLAEDFLKD*IYINIGALKLSANHNIL*IVDVCDDVEKVEK

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_1267 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 10 parental genes, and 16 retrocopies.

Species	Parental gene accession	Retrocopies number
Echinops telfairi	ENSETEG00000019950	1 retrocopy	retro_etel_1009,
Felis catus	ENSFCAG00000003512	1 retrocopy	retro_fcat_172,
Myotis lucifugus	ENSMLUG00000009496	4 retrocopies	retro_mluc_1136, retro_mluc_1499, retro_mluc_1845, retro_mluc_2208,
Monodelphis domestica	ENSMODG00000003743	4 retrocopies	retro_mdom_1519, retro_mdom_1520, retro_mdom_1955, retro_mdom_1956,
Mus musculus	ENSMUSG00000020719	1 retrocopy	retro_mmus_788,
Pteropus vampyrus	ENSPVAG00000001932	1 retrocopy	retro_pvam_1267 ,
Rattus norvegicus	ENSRNOG00000030680	1 retrocopy	retro_rnor_1277,
Tupaia belangeri	ENSTBEG00000009490	1 retrocopy	retro_tbel_4260,
Tarsius syrichta	ENSTSYG00000012149	1 retrocopy	retro_tsyr_1269,
Tursiops truncatus	ENSTTRG00000008793	1 retrocopy	retro_ttru_1662,