RetrogeneDB ID: retro_pvam_1431

Retrocopy location

• Organism: Megabat (Pteropus vampyrus)
• Coordinates: scaffold_84277:571..846(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: TXN2
• Ensembl ID: ENSPVAG00000002012
• Aliases: None
• Description: thioredoxin 2 [Source:HGNC Symbol;Acc:17772]

Sequence

>retro_pvam_1431
CCTGACTTTTGAGATTGAGTTGTCAACAATGGGACAACAATGGACGTGGATTTCTATGCACAGTTGTGTGGCCCCTGCAG
GATCCTAGGGCCAAGGTTAGAGAAGATGGTGGCCATACAGCATAGAAAGATGGTGATGACCAAGAGGTATATTGATGACC
ACACAGATCTCACTATGAGCATGAGGTGTCAGCTCTTCTCACTATGCTGGCCACCAAGAATGGGAATGTGGTGGACAAGC
CTGTGGGCATCAAGGACGAGCTGGAGGCCTTCGTG

Alignment

ORF - retro_pvam_1431 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 68.42 %
• Parental protein coverage: 56.63 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  PDFQDRVVNSETPVVVDFHAQWCGPCKILGPRLEKVVAKQHGKVVMAKVDIDDHTDLAI-EYEVSAVPTV
          PDF.D.VVN..T...VDF.AQ.CGPC.ILGPRLEK.VA.QH.K.VM.K..IDDHTDL...E.EVSA..T.
Retrocopy PDF*D*VVNNGTTMDVDFYAQLCGPCRILGPRLEKMVAIQHRKMVMTKRYIDDHTDLTM<EHEVSALLTM

Parental  LAIKNGDVVDKFVGIKDEDQLEAFL
          LA.KNG.VVDK.VGIKDE..LEAF.
Retrocopy LATKNGNVVDKPVGIKDE--LEAFV

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_1431 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 9 parental genes, and 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Equus caballus	ENSECAG00000013929	1 retrocopy	retro_ecab_229,
Erinaceus europaeus	ENSEEUG00000010654	2 retrocopies	retro_eeur_554, retro_eeur_67,
Homo sapiens	ENSG00000100348	1 retrocopy	retro_hsap_179,
Gorilla gorilla	ENSGGOG00000028091	1 retrocopy	retro_ggor_260,
Myotis lucifugus	ENSMLUG00000015841	1 retrocopy	retro_mluc_483,
Monodelphis domestica	ENSMODG00000000837	2 retrocopies	retro_mdom_1125, retro_mdom_13,
Pteropus vampyrus	ENSPVAG00000002012	1 retrocopy	retro_pvam_1431 ,
Sarcophilus harrisii	ENSSHAG00000000670	1 retrocopy	retro_shar_61,
Tursiops truncatus	ENSTTRG00000006612	1 retrocopy	retro_ttru_438,