RetrogeneDB ID: retro_mdom_379

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 1:325001291..325002181(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMODG00000012897
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: FUCA2
• Ensembl ID: ENSMODG00000017260
• Aliases: None
• Description: fucosidase, alpha-L- 2, plasma [Source:HGNC Symbol;Acc:4008]

Sequence

>retro_mdom_379
TTGGTCCCAGCGTGGGGTCCAGCCCTGCTGCTGCTATTGCTGCTACTGCTGCTCTCCCTGCTCCTGCCAGGATGCTGGGC
ACAGACCAAGATCTATGAGCCCACCTGGGACTCCCTGGATGCCCGTAAACTCCCAGCTTGGTTTGATGAGGACAAGCTTG
GGATCTTCATTCACTGGGGCTCGTTTTCCAAGCCCCGCTTCAGAAGTGAGTGGTTCTGGTGGTACTGGAGACAGCAAAAA
ATTCCAGCCTTTGTAGACTTCATGAAAGTTAACTATCCTCCTGATTTAAAATACGAGGACTTTGCACTGGAATTTAAAGG
AACATTTTTTAATGCCACTCAATGGGCAGATATTTTTCAGGCCTCAGGTGCCAAGTACATTGTCTTGACTACCAAACATC
ATGAAGGTTTCAACCTGTGGAAATCTAAATCTTCATGGAACTGGAATTCTGTTGATAGGGGGCCAAGAAGGGACATTGTA
AAAGAAATGGAAGTAACCATTAGAAATAAGACTGACCTGCACTTTGGCCTGTACTACTCCCTTTTTGAATGGTTCAACCC
CCTTTTCCTTTTGGATAAAGCTAATAAATTCAAGTCAAGAAGGTACCCAGTTGCTAAGTGCCTTCCCGATCTCTATGACC
TGGTGAACACCTACAAGCCTGAGGTTCTCTGGGCAGATGGTGATGGAGATGCATCAGACACCTACAGGAACAGCACTGGC
TTCTTAGCCTGGTTGTATAATGAAGCCCAGTTCCGGATATAGTTGTAACCAATGATCACTGGGGACTTGATAACATCTGC
AGGCATGGTGGCTACTATACCTGCAGTGACTGTTACAACCCTGGATACCTGTTACCTCACAAGTGGGAAAACTGTATGAC
AATAGATAAG

Alignment

ORF - retro_mdom_379 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 82.89 %
• Parental protein coverage: 62.53 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  LVPARGSALLLLSLLLLLSQLLPGCSAQTKRYEPTWDSLDARELPAWFDEAKFGIFIHWGVFSVPGFGSE
          LVPA.G....................AQTK.YEPTWDSLDAR.LPAWFDE.K.GIFIHWG.FS.P.F.SE
Retrocopy LVPAWGPXXXXXXXXXXXXXXXXXXXAQTKIYEPTWDSLDARKLPAWFDEDKLGIFIHWGSFSKPRFRSE

Parental  WFWWYWREQKIPAFVDFMKANYPPDFKYEDFALEFKGTFFKAYQWADIFQASGAKYIVLTTKHHEGFNLW
          WFWWYWR.QKIPAFVDFMK.NYPPD.KYEDFALEFKGTFF.A.QWADIFQASGAKYIVLTTKHHEGFNLW
Retrocopy WFWWYWRQQKIPAFVDFMKVNYPPDLKYEDFALEFKGTFFNATQWADIFQASGAKYIVLTTKHHEGFNLW

Parental  KSNNSWNWNSVDRGPRRDIVKEIEVAIRSKTDLHFGLYYSLFEWFNPLFLLDKANKFKSKRYPVAKSLPD
          KS..SWNWNSVDRGPRRDIVKE.EV.IR.KTDLHFGLYYSLFEWFNPLFLLDKANKFKS.RYPVAK.LPD
Retrocopy KSKSSWNWNSVDRGPRRDIVKEMEVTIRNKTDLHFGLYYSLFEWFNPLFLLDKANKFKSRRYPVAKCLPD

Parental  LYDLVNTYKPEILWADGDGDAPDTYWNSTDFLAWLYNE-SPVRDTVVTNDRWGLDNICRHGGYYTCSDRY
          LYDLVNTYKPE.LWADGDGDA.DTY.NST.FLAWLYNE.SPV.D.VVTND.WGLDNICRHGGYYTCSD.Y
Retrocopy LYDLVNTYKPEVLWADGDGDASDTYRNSTGFLAWLYNE<SPVPDIVVTNDHWGLDNICRHGGYYTCSDCY

Parental  NPGHLLPHKWENCMTIDK
          NPG.LLPHKWENCMTIDK
Retrocopy NPGYLLPHKWENCMTIDK

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	0.36 RPM	0.00 RPM
SRP007412_cerebellum	0.65 RPM	0.00 RPM
SRP007412_heart	0.60 RPM	0.00 RPM
SRP007412_kidney	0.00 RPM	0.00 RPM
SRP007412_liver	1.51 RPM	0.00 RPM
SRP007412_testis	1.38 RPM	0.00 RPM

ChIP-Seq

Monodelphis domestica was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mdom_379 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_379 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	ENSMODG00000017260	1 retrocopy	retro_mdom_379 ,