RetrogeneDB ID: retro_mdom_728

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 2:246305363..246306311(+)
• Located in intron of: ENSMODG00000000233

Retrocopy information

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

Parental gene information

• Parental gene symbol: TFAP2C
• Ensembl ID: ENSMODG00000016445
• Aliases: None
• Description: transcription factor AP-2 gamma (activating enhancer binding protein 2 gamma) [Source:HGNC Symbol;Acc:11744]

Sequence

>retro_mdom_728
GAGAGAATCTCCTTTTGGAACAACCTGGAGGATAGGCATGATGGGAACAGCAATGGGAACCACCACCTCCCTCACCTCCC
AGCTGTCAGTCAGCACCTTTACAGGCCCACAACCCCACCGCTTTCACATTCAGGGGCATCAGACTTCCAGCAGCCTTACT
TTCCCCCGCCCTACCAGCCCTTGCCCTATTCATAGTTTGCTGACCAGTATTCTCACCTGGGTGACCTGTTCTCTATTGAC
CCTCTGCATCAGCTTGCACCAGCTGCCAATAAGCAACAGGCCTGGCCTAACTGCCAGAACCAGGAGCCAGCTGGCTTGAG
CCACCACACAAGACCTGGCCTTGTCCCCCACCTCTCTGGGCTGGATGCTAGAGGACCTGGGCCAAGGAGGGAGACCTACA
GATGTTCAGAGTTGCTCCTACAGCCTCACAGCCATGGGTTAGATGCAACACTGCTGGAAAATCTGGGCTTGCATAATATG
GCCCATCAAATAGAAGATGTACAGAATGTGGAAGACCAACATTTGCTGTTGCATGATCAGACAGTCATCAGGAAAGGTCC
TATTTCAATGACCAAAAGCAACTCCATGGGTCTCCCTTGCCAGAAAGATGGGATGCTAGAATCAGTGGTTAATCATAATG
AAGTATTTTGCTCTGTTCCTGGAACACTTCCTCTTCTCATCCCCAAGTCAAAATATAAAGTGACTGTAGCTGAGGTCCAG
CAAAGACTTTCCTCTCCTGAATGCTTAAATGCCTCCCTGTTAGGTGGTGTCTTCAGAAGAGCCAAATCCAAGAATGGGGG
CCAATCTCTGCAGGAAAAGTTGGATAAACTTGGTTTAAATCTTCCAGCTGAAAGGAGAAAAGCTGCTAATGTGACATTAT
TGACTTCTTTGGTAGAAGGTGAAGCTGTGCATCTGGCCTGAGATTTTGGTTATGTCTGTGAAACTGAA

Alignment

ORF - retro_mdom_728 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 84.49 %
• Parental protein coverage: 70.69 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  DNVKYEEDCEDRHDGNSNGNPRLPHLPAVSQHLYSPAAPPLSHSGASDFQPPYFPPPYQPLPYSQSADPY
          .........EDRHDGNSNGN..LPHLPAVSQHLY.P..PPLSHSGASDFQ.PYFPPPYQPLPYS..AD.Y
Retrocopy ERISFWNNLEDRHDGNSNGNHHLPHLPAVSQHLYRPTTPPLSHSGASDFQQPYFPPPYQPLPYS*FADQY

Parental  SHLADPFSINPLHQPAPAASQQQAWPSRQNQEPAGLSHHTRPGLVPHLSGLDAGGPGARRETYRRSELLL
          SHL.D.FSI.PLHQ.APAA..QQAWP..QNQEPAGLSHHTRPGLVPHLSGLDA.GPG.RRETYR.SELLL
Retrocopy SHLGDLFSIDPLHQLAPAANKQQAWPNCQNQEPAGLSHHTRPGLVPHLSGLDARGPGPRRETYRCSELLL

Parental  QPHGHGLDAALVENLGLHDMAHQMEDVQNVEDQHLLLHDQTVIRKGPISMTKSNSLGIPCQKDGMLGSVV
          QPH.HGLDA.L.ENLGLH.MAHQ.EDVQNVEDQHLLLHDQTVIRKGPISMTKSNS.G.PCQKDGML.SVV
Retrocopy QPHSHGLDATLLENLGLHNMAHQIEDVQNVEDQHLLLHDQTVIRKGPISMTKSNSMGLPCQKDGMLESVV

Parental  NHNEVFCSVPGRLSLLSSTSKYKVTVAEVQRRLSSPECLNASLLGGVLRRAKSKNGGRSLREKLDKIGLN
          NHNEVFCSVPG.L.LL...SKYKVTVAEVQ.RLSSPECLNASLLGGV.RRAKSKNGG.SL.EKLDK.GLN
Retrocopy NHNEVFCSVPGTLPLLIPKSKYKVTVAEVQQRLSSPECLNASLLGGVFRRAKSKNGGQSLQEKLDKLGLN

Parental  LPAGRRKAANVTLLTSLVEGEAVHLARDFGYVCETE
          LPA.RRKAANVTLLTSLVEGEAVHLA.DFGYVCETE
Retrocopy LPAERRKAANVTLLTSLVEGEAVHLA*DFGYVCETE

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	8.22 RPM
SRP007412_cerebellum	0.00 RPM	0.65 RPM
SRP007412_heart	0.00 RPM	1.59 RPM
SRP007412_kidney	0.00 RPM	0.00 RPM
SRP007412_liver	0.00 RPM	0.00 RPM
SRP007412_testis	0.00 RPM	1.18 RPM

ChIP-Seq

Monodelphis domestica was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mdom_728 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_728 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 8 parental genes, and 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000011025	1 retrocopy	retro_chof_1226,
Macropus eugenii	ENSMEUG00000007703	1 retrocopy	retro_meug_166,
Myotis lucifugus	ENSMLUG00000010003	2 retrocopies	retro_mluc_284, retro_mluc_5,
Monodelphis domestica	ENSMODG00000016445	1 retrocopy	retro_mdom_728 ,
Otolemur garnettii	ENSOGAG00000033901	1 retrocopy	retro_ogar_1767,
Pan troglodytes	ENSPTRG00000013654	1 retrocopy	retro_ptro_1933,
Ictidomys tridecemlineatus	ENSSTOG00000014299	3 retrocopies	retro_itri_1741, retro_itri_1801, retro_itri_1813,
Tursiops truncatus	ENSTTRG00000005983	1 retrocopy	retro_ttru_535,