RetrogeneDB ID: retro_mdom_447

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 1:590820091..590820780(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SNRPA
• Ensembl ID: ENSMODG00000007912
• Aliases: None
• Description: small nuclear ribonucleoprotein polypeptide A [Source:HGNC Symbol;Acc:11151]

Sequence

>retro_mdom_447
CTCCAGATGAGAGGCCATGCATTTGTCATCTTCAAGGAGATCAGCAGTGCTACTGACATGCTGAGATCTATGCAGAGATT
TCCCTCCTATGACAAACCCTTGAGAATCCAATATACCAAGTCAGACTTGGACATCATTGTCAAGATGATGGGCATGTACA
TGGTGTGGGACTGGACACTCAAGAAAAGAAAGCTCAAGGGCTTGGAAACAACTGCAGTCAAGAAGACTGTTCTGGGTGTG
ATGGTAACCCATGTTGTGGCTGCTATCTAGCCTGCCCCAGGAATGCCACCCATGATCCAGGCCCCCCTGCATCATACAGC
ATCTTCCAGAGAAGCGACTTTATATGCTTCCACCAAGTATGATCCACACCCCTGGAGAGATACCACTTGGGGCCATGACC
CCAAAGCAGATGATGCCTGGATAGATGCCATCCACCCAGCTGCTTTCTGAAAACCCACTGAACCATATCCTGTTCCTCAC
CAACCTGCCAGAGGAGACCAATGAACTCATGCTGTCTGTGCTTCTTCAATCAGTTTGCTAGCTTCAAAGAGGGGCCTCTG
GTGCCCAGGCATCAAGACATTGCTCTTGTGGAGTTTGACAAGGAGGTACAGGCTGGAGCTGCCTGAGATGCCCTGCAGGG
CTTCAAAATCATCCATAACGCTGCCATGAAAATTTCTTTTGCCAAGGAG

Alignment

ORF - retro_mdom_447 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 68.51 %
• Parental protein coverage: 81.18 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  LKMRGQAFVIFKEISSATNALRSMQGFPFYDKPMRIQYAKSDSDIIAKMKGTYVERDRKREKRKPKGQET
          L.MRG.AFVIFKEISSAT..LRSMQ.FP.YDKP.RIQY.KSD.DII.KM.G.Y...D....KRK.KG.ET
Retrocopy LQMRGHAFVIFKEISSATDMLRSMQRFPSYDKPLRIQYTKSDLDIIVKMMGMYMVWDWTLKKRKLKGLET

Parental  PAVKKAVPGGAAAPVVAAVQPVPGMPPMTQAPR-IMHHLPGQPPYMPPPGMIPPPGLAPGQIPPGAMPPQ
          .AVKK.V.G.....VVAA..P.PGMPPM.QAP..I..HLP....YM.PP.MI..PG.....IP.GAM.P.
Retrocopy TAVKKTVLGVMVTHVVAAI*PAPGMPPMIQAPL>IIQHLPEKRLYMLPPSMIHTPG----EIPLGAMTPK

Parental  QMMPGQMPPAQPLSENPPNHILFLTNLPEETNELMLSML-FNQFPGFKEVRLVPGRHDIAFVEFDNEVQA
          QMMPG.MP..Q.LSENP.NHILFLTNLPEETNELMLS.L.FNQF..FKE..LVP...DIA.VEFD.EVQA
Retrocopy QMMPG*MPSTQLLSENPLNHILFLTNLPEETNELMLSVL>FNQFASFKEGPLVPRHQDIALVEFDKEVQA

Parental  GAARDALQGFKITQNNAMKISFAKK
          GAA.DALQGFKI..N.AMKISFAK.
Retrocopy GAA*DALQGFKIIHNAAMKISFAKE

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	0.24 RPM	0.00 RPM
SRP007412_cerebellum	0.33 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_447 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_447 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 9 parental genes, and 14 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000005091	1 retrocopy	retro_cfam_1114,
Callithrix jacchus	ENSCJAG00000014865	1 retrocopy	retro_cjac_287,
Cavia porcellus	ENSCPOG00000010875	1 retrocopy	retro_cpor_663,
Myotis lucifugus	ENSMLUG00000000219	1 retrocopy	retro_mluc_1517,
Monodelphis domestica	ENSMODG00000007912	1 retrocopy	retro_mdom_447 ,
Mustela putorius furo	ENSMPUG00000017681	1 retrocopy	retro_mputfur_593,
Mus musculus	ENSMUSG00000061479	6 retrocopies	retro_mmus_275, retro_mmus_3374, retro_mmus_469, retro_mmus_888, retro_mmus_889, retro_mmus_958,
Otolemur garnettii	ENSOGAG00000002864	1 retrocopy	retro_ogar_2046,
Pteropus vampyrus	ENSPVAG00000001494	1 retrocopy	retro_pvam_832,