RetrogeneDB ID: retro_mdom_1096

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 3:94213166..94213749(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SDF2L1
• Ensembl ID: ENSMODG00000017698
• Aliases: None
• Description: stromal cell-derived factor 2-like 1 [Source:HGNC Symbol;Acc:10676]

Sequence

>retro_mdom_1096
TCTGCCCTGACTTGGGTTGGGGTAGAGCTTAGACAGGGGCCACAACCTATGGGTCCATGTTGAAGCTGCTCAACAAGTGC
AATGGCATCCAGCTAAACTCTCGTGACTTCAAATATGACTCTGGGAGTGGACAGCAGTATGTTGACAGGAGTTGAGGGCT
CAGAAGATGCCAACAGCTACTGGAAAATTCAAGGTGGGAGAGAGGCAGATGCTTGCAAGAGGTGTCAGTGATCTGTGTTA
AAGCTGGCCAACTGACCCATGTGAACATGGGTAAGAACCAGCATGCCCACTGCTTCTCCTCCCTTTTTTGTAACAGTCAG
GAAGGGAATACCTTCAGAGATGGTGGCGAGGGAGACTAGATGAATATTTGGCTGATGCAATGCAATAGGGTCTACTGAAA
TCTGCAGGAAGCTGTCCACTTCCAATATGCTGGTACCCACATCAATTTTTCCATCACGGGGGAGCACTATAGGCATTCCA
CCTGAAAGTAGAGGGAGGTCCACAGCATGTCCATCTCAACCACCACAATTCTTGGAAAGCAATGGAGTGTGCCTTCATCA
AGCTCAGACCCACACAGTCTTCC

Alignment

ORF - retro_mdom_1096 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 55.45 %
• Parental protein coverage: 89.59 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  AAGTEAGAELG-TGAVTCGSVLKLLNTRHGVRLHSHDSDLFLASAGSGQQSV-TGVEGSEDANSYWRIRG
          .A.T..G.EL..TGA.T.GS.LKLLN...G..L.S.D...F....GSGQQ.V.TGVEGSEDANSYW.I.G
Retrocopy SALTWVGVELR<TGATTYGSMLKLLNKCNGIQLNSRD---FKYDSGSGQQYV>TGVEGSEDANSYWKIQG

Parental  GAE-GECPRGVPVRCGQAVRLTHVNTGKNLHTHHFPSPLSNNQEVSAFGDSGEGDQLDVWLVQCSGAYWD
          G.E.G.C...V.V.C..A..LTHVN.GKN.H.H.F.S...N.QE...F.D.GEGD....WL.QC...Y..
Retrocopy GRE<GRCLQEVSVICVKAGQLTHVNMGKNQHAHCFSSLFCNSQEGNTFRDGGEGD*MNIWLMQCNRVY*N

Parental  REEAVRFQHAGTHVYLSVTGEQYGHPIRGQREVHGMPSP-NQHNSWKAMEGVFIKPSPTDSS
          ..EAV.FQ.AGTH...S.TGE.Y.H.....REVH.M....N.HNSWKAME..FIK..PT.SS
Retrocopy LQEAVHFQYAGTHINFSITGEHYRHST*K*REVHSMSIS<NHHNSWKAMECAFIKLRPTQSS

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_1096 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_1096 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.

---

Parental genes homology:

Parental genes homology involve 1 parental gene, and 1 retrocopy.

Species	Parental gene accession	Retrocopies number
Monodelphis domestica	ENSMODG00000017698	1 retrocopy	retro_mdom_1096 ,