RetrogeneDB ID: retro_mdom_1427

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 4:426943153..426943606(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: AP1S3
• Ensembl ID: ENSMODG00000021198
• Aliases: None
• Description: adaptor-related protein complex 1, sigma 3 subunit [Source:HGNC Symbol;Acc:18971]

Sequence

>retro_mdom_1427
TTTCATGTTGCGCTCAGTTGACAAGAGAAGGGAAGGCTGCAAAAGTGGCATGCCATATTTCCTGATAAAGAGAGAGAAAA
GATTATCTGAGAAATTGTACAGATGATTCTATCTTGTGGCCAAAAGATGAGCAGTTTTGTTGACTGGAAAGATCTAAAAT
TTGTTTATAAAAGATACTCTAGCTCATATTTTGGCTGCTCAGTAGAAAATCAGGACAATGAACTGTTGGCAGTAGAGATC
ATACATCGTTATGTGGAATTACTAGACAAGTATTTTGGAAATGTCTGTGAACCAGATATTATATTTAATTTTGAAAAGGC
AGATTTTATCCTTGATGAGTTTATATTGGGTGGAGAAATCCAGGAAACCTCAAAGAAGTCTGCTGTCAAGACTGTTGAAG
ACTCTGATGTGTCACAGGAGACAATGGAGTAATACACAGCGAGGCTGTATTTT

Alignment

ORF - retro_mdom_1427 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 75.5 %
• Parental protein coverage: 61.38 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  FILLFSRQGKLRLQKWYTTLPDKERKKIIREIVQMILSRGQRTSSFVDWKDLKLVYKRYASLYFCCAVEN
          F....S.Q.K.RLQKW....PDKER.KII.EIVQMILS.GQ..SSFVDWKDLK.VYKRY.S.YF.C.VEN
Retrocopy FHVALS*QEKGRLQKWHAIFPDKEREKII*EIVQMILSCGQKMSSFVDWKDLKFVYKRYSSSYFGCSVEN

Parental  QDNELLTLEIVHRYVELLDKYFGNVCELDIIFNFEKAYFILDEFIMGGEIQETSKKSAVKAIEDSDMLQE
          QDNELL..EI.HRYVELLDKYFGNVCE.DIIFNFEKA.FILDEFI.GGEIQETSKKSAVK..EDSD..QE
Retrocopy QDNELLAVEIIHRYVELLDKYFGNVCEPDIIFNFEKADFILDEFILGGEIQETSKKSAVKTVEDSDVSQE

Parental  TMEEYMSKPAF
          TME.Y.....F
Retrocopy TME*YTARLYF

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_1427 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_1427 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 11 parental genes, and 34 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000011939	5 retrocopies	retro_chof_113, retro_chof_1230, retro_chof_1299, retro_chof_1949, retro_chof_2099,
Callithrix jacchus	ENSCJAG00000012352	2 retrocopies	retro_cjac_3187, retro_cjac_3903,
Macropus eugenii	ENSMEUG00000016580	11 retrocopies	retro_meug_1074, retro_meug_1342, retro_meug_1488, retro_meug_168, retro_meug_1864, retro_meug_289, retro_meug_318, retro_meug_361, retro_meug_816, retro_meug_909, retro_meug_938,
Microcebus murinus	ENSMICG00000014406	1 retrocopy	retro_mmur_1492,
Monodelphis domestica	ENSMODG00000017197	7 retrocopies	retro_mdom_1189, retro_mdom_1329, retro_mdom_1441, retro_mdom_1470, retro_mdom_1616, retro_mdom_1987, retro_mdom_903,
Monodelphis domestica	ENSMODG00000017579	1 retrocopy	retro_mdom_1774,
Monodelphis domestica	ENSMODG00000021198	1 retrocopy	retro_mdom_1427 ,
Mus musculus	ENSMUSG00000054702	3 retrocopies	retro_mmus_2202, retro_mmus_2799, retro_mmus_487,
Ochotona princeps	ENSOPRG00000013358	1 retrocopy	retro_opri_443,
Pan troglodytes	ENSPTRG00000012979	1 retrocopy	retro_ptro_2258,
Sarcophilus harrisii	ENSSHAG00000010973	1 retrocopy	retro_shar_695,