RetrogeneDB ID: retro_mdom_919

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 2:434410498..434411007(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: VAPB
• Ensembl ID: ENSMODG00000016549
• Aliases: None
• Description: VAMP (vesicle-associated membrane protein)-associated protein B and C [Source:HGNC Symbol;Acc:12649]

Sequence

>retro_mdom_919
ATAAAGCCTTTTGAAAATGATCCTAATGAGAAAAGTAAACACAAGTTTATGTTTCAATCTATATTTGCTCTAATAGATAA
CTTCAGATTTGGAAGCAGAATGGAAGGAGGAAAAGCCAGAAGATCTTATGGATTCAAAACGTAGATAGGTGTTTAAATTG
CCAAAAAGGAATGATAAACCACGTGATACAGAAATAAATAAAATGATGTCCACTATGGCAAGAAAGACAAAATCATTTAT
TATGTCTAAATTTGTAAGTTCTTCTTTATATGATACTGAAGCTAAGAAAGTAATAGACAAATGTAAAAGGCTGCAGGCAG
AAGTTCAGAGATTATAGGAAGAAGAAAAACATTTTAAGGAAAAAGATGGGCTGCAGATGAGAAAAAAACAGAAGCACAAC
AGCCCAGCTTCTGTTTTAGGTACCTTGTGAAGAAGAAGGGCTTATAACTGGGCTTCTGGCTCTCTTACTTTTCTTATTGT
CAGTAAAATTATAGGGAAAAATCTCCTTA

Alignment

ORF - retro_mdom_919 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 64.37 %
• Parental protein coverage: 70.12 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  LQPFDYDPNEKSKHKFMVQSMFAPTD-TSDMEAV--EAKPEDLMDSKLRCVFELPAENDKPHDVEINKIM
          ..PF..DPNEKSKHKFM.QS.FA..D.TSD.EA...E.KPEDLMDSK.R.VF.LP..NDKP.D.EINK.M
Retrocopy IKPFENDPNEKSKHKFMFQSIFALID>TSDLEAEWKEEKPEDLMDSKRR*VFKLPKRNDKPRDTEINKMM

Parental  STTATKTESSVMSKSISSSLDDTEAKKVMEECKRLQVEVQRLQEENKQFKEEDGLRMRKTLQSNSPASTA
          ST.A.KT.S..MSK..SSSL.DTEAKKV...CKRLQ.EVQRL.EE.K.FKE.DGL.MRK....NSPAS..
Retrocopy STMARKTKSFIMSKFVSSSLYDTEAKKVIDKCKRLQAEVQRL*EEEKHFKEKDGLQMRKKQKHNSPASVL

Parental  AT-IVKE-EGLSTRLLALVVLFFIVGVIIGKIAL
          .T..VK..EGL.T.LLAL..LF.......GKI.L
Retrocopy GT<LVKK<EGLITGLLAL-LLFLLSVKL*GKISL

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Expression validation based on RNA-Seq data:

Library	Retrocopy expression	Parental gene expression
SRP007412_brain	0.00 RPM	161.63 RPM
SRP007412_cerebellum	0.00 RPM	126.01 RPM
SRP007412_heart	0.00 RPM	78.74 RPM
SRP007412_kidney	0.00 RPM	96.13 RPM
SRP007412_liver	0.00 RPM	78.54 RPM
SRP007412_testis	0.00 RPM	11.98 RPM

ChIP-Seq

Monodelphis domestica was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mdom_919 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_919 was not experimentally validated.

Homology

Retrocopy orthology:

Monodelphis domestica 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 7 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000017424	1 retrocopy	retro_btau_1010,
Dasypus novemcinctus	ENSDNOG00000012711	1 retrocopy	retro_dnov_206,
Echinops telfairi	ENSETEG00000017229	1 retrocopy	retro_etel_1235,
Macropus eugenii	ENSMEUG00000009788	1 retrocopy	retro_meug_842,
Monodelphis domestica	ENSMODG00000016549	1 retrocopy	retro_mdom_919 ,
Monodelphis domestica	ENSMODG00000021442	1 retrocopy	retro_mdom_57,
Nomascus leucogenys	ENSNLEG00000009351	1 retrocopy	retro_nleu_55,