RetrogeneDB ID: retro_mdom_1050

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 3:379369172..379369844(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: ACPP
• Ensembl ID: ENSMODG00000011756
• Aliases: None
• Description: acid phosphatase, prostate [Source:HGNC Symbol;Acc:125]

Sequence

>retro_mdom_1050
CTATTTCAACATGGAGACCGGAGTCCCATTGAAACCTTTCCGAAAAATCCCTATCAAGAATCTGCTTGGCCTCGGGGATT
TGGACAACTTAGTCTGCTTGGGATGGAGCCGCACTATGAGCTTGGAACATATTTAAGGAAAAGATATTCCAAATTCTTGA
ATTCCACTTACAATCAGAATGAGGTTTAGGTCCGAAGCACAGACGTTGACTGGACCCTGATGAGTGCCATGACCAATCTT
GTTGCCCTCTTTCCACCAGAAGGCCCAAGTATTTGGAACCCCCAAATCCTTTGGCAGCCGATTCCAGTTCATACAGTGCC
AACTTCTGAAGATCAGTTGCTGTACCTTCCTGATATAAAATGCCCTCGACTTCAAGAGCTTCAGGGAGAAACTTTGAGGT
CAAAGGAATATCAAAACTTGCTGTCTCCATACAAGGATTTTATAAGTACTTTACCAGCACTTTCAGGACTCGAAATCAAG
GACCTTAATGGAATTTGGAATAAAATCTATGAACCTTTATTTTGTGAGAGAGTTCACAATTTTACTCTACCCTCCTGGGC
CACTGCAGACACAATGGCAAAGCTGGAGGAGCTGTCCAAATTATCTCTCTTGTCAACCTTTGGAATTTATAAGCAGAAAG
AAAAGGCTCGACTTCAGGGAGGTGTTCTGGTG

Alignment

ORF - retro_mdom_1050 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 95.58 %
• Parental protein coverage: 59.47 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  LFRHGDRSPIETFPKDPYQESAWPRGFGQLSLLGMEQHYELGTYLRKRYSKFLNSTYNRNEATVYVRSTD
          LF.HGDRSPIETFPK.PYQESAWPRGFGQLSLLGME.HYELGTYLRKRYSKFLNSTYN.NE..V.VRSTD
Retrocopy LFQHGDRSPIETFPKNPYQESAWPRGFGQLSLLGMEPHYELGTYLRKRYSKFLNSTYNQNE--V*VRSTD

Parental  VDRTLMSAMTNLAALFPPEGPSIWNPQILWQPIPVHTVPTSEDQLLYLPDIKCPRLQELQGETLRSKEYQ
          VD.TLMSAMTNL.ALFPPEGPSIWNPQILWQPIPVHTVPTSEDQLLYLPDIKCPRLQELQGETLRSKEYQ
Retrocopy VDWTLMSAMTNLVALFPPEGPSIWNPQILWQPIPVHTVPTSEDQLLYLPDIKCPRLQELQGETLRSKEYQ

Parental  NLLSPYKDFISTLPALSGLEIKDLNGIWNKIYDPLFCERVHNFTLPSWATADTMAKLEELSKLSLLSTFG
          NLLSPYKDFISTLPALSGLEIKDLNGIWNKIY.PLFCERVHNFTLPSWATADTMAKLEELSKLSLLSTFG
Retrocopy NLLSPYKDFISTLPALSGLEIKDLNGIWNKIYEPLFCERVHNFTLPSWATADTMAKLEELSKLSLLSTFG

Parental  IYKQKEKARLQGGVLV
          IYKQKEKARLQGGVLV
Retrocopy IYKQKEKARLQGGVLV

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	0.00 RPM
SRP007412_cerebellum	0.00 RPM	0.00 RPM
SRP007412_heart	0.00 RPM	0.00 RPM
SRP007412_kidney	0.00 RPM	0.00 RPM
SRP007412_liver	0.00 RPM	0.00 RPM
SRP007412_testis	0.00 RPM	0.00 RPM

ChIP-Seq

Monodelphis domestica was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mdom_1050 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_1050 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	ENSMODG00000011756	1 retrocopy	retro_mdom_1050 ,