RetrogeneDB ID: retro_pvam_524

Retrocopy location

• Organism: Megabat (Pteropus vampyrus)
• Coordinates: GeneScaffold_3605:1193..2364(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SMS
• Ensembl ID: ENSPVAG00000016785
• Aliases: None
• Description: spermine synthase [Source:HGNC Symbol;Acc:11123]

Sequence

>retro_pvam_524
CCCGCGCGGCCCTCTTCATCCCCTTCCGTCTCCCATAGCCGCCTCCCTCAGGCCCGCCTCAGGGCCGGGTCTCACTATGA
CAGCAGCGCGACACAGCACACTCGACTTCCTGCTGGGCGCCCTAGCCGGCTGCGAGACCATTCTAAAAGGCCTGCGGTCC
ATTTTCCAGGAGCAGGGGATGACCGAGTCGCTGCACACCTGGCAGGACCATGGCTATTTAGTGAACTACATCAACAAAAA
CGGCAGCTTTGCCAACTTGTGAATTGACTCACGTGGTTTGATGTCGCTGGACCTTCAGAGTTACAGTGGCGATGCGCAAG
CCAAAGAAGTTGACGGTCTTTTGAACAAAGTAGAAGGAAGAATGAAATAATTGAATCAGGACAGCCCCTGTCAGGTGAAA
CGATTACCACCCATAGTTCGAGGAGGGGCCGTCGACAGATACTGGCCTACTGCTGATGGCCGCCTGGTTGAGTATGACAT
AGATGAAGTGGCAGATGATGAAGATTCGCCTTATCAGAATATTAAAATTCTACATTCAAAACAATATGGAAATATTCTCA
TCCTGAGTGGGGATGTAAATCTGGCAGAGAGTGATTGGGGGTATACCCAGGCCATCATAGGCAGTGGTAAAGAGGCTTAC
GCTGGCAAAGACGTGCTGATTCTGGGTGGTGGAGATGGGGGCGTATTACATGAAGTAGTCAAACCGAAACCAAAGATGGC
CACTATGGTAGAGATTGACCAAATGGTGATTGACGGATGTACGAAATACATGTGAAAAACGTGTGGCGATATCTTGGATG
ATCTTACAGGAGACTGCTATCGGGTTCTCAGAGAATACTGTGTTCCAGCACTGAAGAGGTACACCAAAGAAGGCGGAGAG
TTTGATTATGTGATTAATGATTTGACGGCTGTTCCAATCCCCACTTCTCCAGAAGAAGATTCCACATAGGAGTTTCTCAG
GCTGATTCTTGACCTATCAATGAGAGTACTGAAGCAGGATGGGAAGTGTTTTACACAAGGGAACTGTGTCAATTTGACAG
AAGCCCTTTCACTCTATGAAGAACAACTCCAGTGCCTATATTGTCCTGTGGAATTCTCAAAGGAGGTCGTCTGCGTCCCT
TTGTACTTCGAGTTGTGAGTATTTTACACAGTTTGAAAGAAAGCCCAGCCT

Alignment

ORF - retro_pvam_524 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 78.26 %
• Parental protein coverage: 97.99 %
• Number of stop codons detected: 6
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  PEPDPCGPPVSRGRSP-RHGPGPLLTMAAARHSTLDFMLGAKADGETILKGLQSIFQEEGMTESVHTWQD
          P......P.VS..R.P.R...GP.LTM.AARHSTLDF.LGA.A..ETILKGL.SIFQE.GMTES.HTWQD
Retrocopy PARPSSSPSVSHSRLP>RPASGPGLTMTAARHSTLDFLLGALAGCETILKGLRSIFQEQGMTESLHTWQD

Parental  HGYLATYINKNGSFVNLRIYPHGLVLLDLQSYDGDTEGKEVDSLLNKVEERMKELSQDSTGRVKRLPPLV
          HGYL..YINKNGSF.NL.I...GL..LDLQSY.GD...KEVD.LLNKVE.RMK.L.QDS...VKRLPP.V
Retrocopy HGYLVNYINKNGSFANL*IDSRGLMSLDLQSYSGDAQAKEVDGLLNKVEGRMK*LNQDSPCQVKRLPPIV

Parental  RGGAIDRYWPTADGRLVEYDIDEVVYDEDSPYQNIKILHSKQFGNILILNGDVNLAESDLAYTRAIMGSG
          RGGA.DRYWPTADGRLVEYDIDEV..DEDSPYQNIKILHSKQ.GNILIL.GDVNLAESD..YT.AI.GSG
Retrocopy RGGAVDRYWPTADGRLVEYDIDEVADDEDSPYQNIKILHSKQYGNILILSGDVNLAESDWGYTQAIIGSG

Parental  KEDYTGKDVLILGGGDGGILCEIVKLKPKMVTMVEIDQMVIDGCKKYMRKTCGDVLDNLKGDCYQVLIED
          KE.Y.GKDVLILGGGDGG.L.E.VK.KPKM.TMVEIDQMVIDGC.KYM.KTCGD.LD.L.GDCY.VL.E.
Retrocopy KEAYAGKDVLILGGGDGGVLHEVVKPKPKMATMVEIDQMVIDGCTKYM*KTCGDILDDLTGDCYRVLREY

Parental  CIPVLKRYAKEGREFDYVINDLTAVPISTSPEEDSTWEFLRLILDLSMKVLKQDGKYFTQGNCVNLTEAL
          C.P.LKRY.KEG.EFDYVINDLTAVPI.TSPEEDST.EFLRLILDLSM.VLKQDGK.FTQGNCVNLTEAL
Retrocopy CVPALKRYTKEGGEFDYVINDLTAVPIPTSPEEDST*EFLRLILDLSMRVLKQDGKCFTQGNCVNLTEAL

Parental  SLYEEQLGRLYCPVEFSKEIICVPSYLELWVFYTVWKKAKP
          SLYEEQL..LYCPVEFSKE..CVP.Y.EL.VFYTV.KKA.P
Retrocopy SLYEEQLQCLYCPVEFSKEVVCVPLYFEL*VFYTV*KKAQP

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_524 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 13 parental genes, and 26 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000018382	1 retrocopy	retro_btau_1412,
Canis familiaris	ENSCAFG00000013284	3 retrocopies	retro_cfam_1076, retro_cfam_1995, retro_cfam_613,
Callithrix jacchus	ENSCJAG00000033933	1 retrocopy	retro_cjac_518,
Echinops telfairi	ENSETEG00000010098	2 retrocopies	retro_etel_1066, retro_etel_1540,
Gorilla gorilla	ENSGGOG00000003123	3 retrocopies	retro_ggor_1335, retro_ggor_2437, retro_ggor_3009,
Myotis lucifugus	ENSMLUG00000013185	3 retrocopies	retro_mluc_471, retro_mluc_530, retro_mluc_92,
Macaca mulatta	ENSMMUG00000020392	2 retrocopies	retro_mmul_2003, retro_mmul_2574,
Monodelphis domestica	ENSMODG00000007897	1 retrocopy	retro_mdom_412,
Oryctolagus cuniculus	ENSOCUG00000006016	2 retrocopies	retro_ocun_1458, retro_ocun_1918,
Pongo abelii	ENSPPYG00000020182	4 retrocopies	retro_pabe_2649, retro_pabe_2810, retro_pabe_3752, retro_pabe_38,
Pteropus vampyrus	ENSPVAG00000016785	1 retrocopy	retro_pvam_524 ,
Rattus norvegicus	ENSRNOG00000007688	2 retrocopies	retro_rnor_1934, retro_rnor_938,
Vicugna pacos	ENSVPAG00000007543	1 retrocopy	retro_vpac_50,