RetrogeneDB ID: retro_mdom_1521

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 5:104282800..104283754(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SLC2A10
• Ensembl ID: ENSMODG00000016232
• Aliases: None
• Description: solute carrier family 2 (facilitated glucose transporter), member 10 [Source:HGNC Symbol;Acc:13444]

Sequence

>retro_mdom_1521
AACAGGAAGAAATAGTACTCTTTCTTGAGCCTCTTTAGGGCCAAGGCCAACATGCAGAGTTGAACAGCCGTGGCTCTGGG
TCTTGTGCTCTTCCAATAGCTCACCAGACAACCCAATGTGCTCTGCTCTGCATCCACCATTTTCCATTCCGTGGGTTTTC
AAGGGGGCTCTTCCAGTACCCTAGCTTCTGTGGGACTCAAAGGGGTAGAAGTGGCTGCTACCTTGGTGGCTATTGAACTG
GTGGACTGTGCTGGGAGGGGGGTACTGCTGATGGCTGGCTGTGCTGTCATGGCTGTCTCAGTCAGTGGCATTGGGCTGGT
TGGTTTTACTGTGTCAATGGACCCCACTCAGGGCTGCCACAGACCTCCTGAGACATCCAACACGACCACTGCCTCCAGGT
TTCCTGCTTTCCACACAGACCCCAGCCTACCCTCTCTCCAAGGGAGCTCAGACTATCCTGACATAGGATTGACTTCCCTA
AAGATGGACACATCTGGTGCCAGAGCCGAAGGGACAGTTGCTAATTCCTCGGGAGTTCAGGGAGCTGTTCTTCCAGCTCA
TGAATCACTGGCACATGGCACCAGTAACCTGGTTACCAACTCCTAGACTAGCAGGCACAGGGTCTTAAACTGGATTGCTT
TACTCTACATGATGGCATTCGTGAGTGCCTTTTCTTTTGGATTTAGACCAATCACCTGGCTGGTCCTCAGTGAGATCAAT
CCAGCTGAAATTTGAGGATGGGCATTTGCCTTCTGCAACAGTTTTAAATGGGCTTCCAACTTGCTGATCAGCCTCTCCTT
CCTGGATATGATTGGAGCCATTGGCTTATCCTGGACCTTCCTGCTATATGGTCTGATGGCTGTGGCTGGCCTTGGTTTCA
TTTATTCATTTGTCCCTGAAACCAAAGGCCAGTCCCTGGCAGAGATAGACCAACAGTTCCAGAGAAGACAGTTC

Alignment

ORF - retro_mdom_1521 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 88.36 %
• Parental protein coverage: 59.33 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  HRKEQYSFWSLFRAKANMRSRTAVGLGLVLFQQLTGQPNVLCYASTIFHSVGFRGGSSATLASVGLGGVK
          .RK..YSF.SLFRAKANM.S.TAV.LGLVLFQ.LT.QPNVLC.ASTIFHSVGF.GGSS.TLASVGL.GV.
Retrocopy NRKK*YSFLSLFRAKANMQS*TAVALGLVLFQ*LTRQPNVLCSASTIFHSVGFQGGSSSTLASVGLKGVE

Parental  VAATLVAMGLVDRAGRRVLLMAGCAVMAVSVSGIGLVGFTVSMDPTQGCHRPPETSNMTTASRFPAFQAD
          VAATLVA..LVD.AGR.VLLMAGCAVMAVSVSGIGLVGFTVSMDPTQGCHRPPETSN.TTASRFPAF..D
Retrocopy VAATLVAIELVDCAGRGVLLMAGCAVMAVSVSGIGLVGFTVSMDPTQGCHRPPETSNTTTASRFPAFHTD

Parental  PSLPPLQGSSDYPDIGLTSLKMDTSGARAKGTVANSSGVQGALLPAHDSLAHGTSNLVTNSWTSRHRVLN
          PSLP.LQGSSDYPDIGLTSLKMDTSGARA.GTVANSSGVQGA.LPAH.SLAHGTSNLVTNS.TSRHRVLN
Retrocopy PSLPSLQGSSDYPDIGLTSLKMDTSGARAEGTVANSSGVQGAVLPAHESLAHGTSNLVTNS*TSRHRVLN

Parental  WIALLCMMAFVSAFSFGFGPITWLVLSEIYPAEIRGRAFAFCNSFNWAANLLISLSFLDLIGAIGLSWTF
          WIALL.MMAFVSAFSFGF.PITWLVLSEI.PAEI.G.AFAFCNSF.WA.NLLISLSFLD.IGAIGLSWTF
Retrocopy WIALLYMMAFVSAFSFGFRPITWLVLSEINPAEI*GWAFAFCNSFKWASNLLISLSFLDMIGAIGLSWTF

Parental  LLYGLMAVAGLGFIYLFVPETKGQSLAEIDQQFQRRRY
          LLYGLMAVAGLGFIY.FVPETKGQSLAEIDQQFQRR..
Retrocopy LLYGLMAVAGLGFIYSFVPETKGQSLAEIDQQFQRRQF

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	10.97 RPM
SRP007412_cerebellum	0.00 RPM	23.50 RPM
SRP007412_heart	0.00 RPM	20.93 RPM
SRP007412_kidney	0.00 RPM	31.60 RPM
SRP007412_liver	0.00 RPM	69.48 RPM
SRP007412_testis	0.00 RPM	14.54 RPM

ChIP-Seq

Monodelphis domestica was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mdom_1521 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_1521 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 1 parental gene, and 1 retrocopy.

Species	Parental gene accession	Retrocopies number
Monodelphis domestica	ENSMODG00000016232	1 retrocopy	retro_mdom_1521 ,