RetrogeneDB ID: retro_mdom_1226

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 4:25410720..25411246(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: EAPP
• Ensembl ID: ENSMODG00000014525
• Aliases: None
• Description: E2F-associated phosphoprotein [Source:HGNC Symbol;Acc:19312]

Sequence

>retro_mdom_1226
TCTGAGGATGATGACCCATAGGTAGTTAAGCGTCCAGCAATAGGAAACCAGTTTTGAGTTGTTCTGAACAGGAAGTAGAT
GTGTTTTTACATGGCGCTCCTGACCAAAAAGGAAAACCCATCAGAGAATGTCTTCCTGGTGAAAGTGAACCGTGGTGTGA
AGATGAGTTTGAAAATAAATGGAAGCTGAATTAAATTTCACCATAAAAACAATGGAAGAGAAGTTGACCCCACTAGAAAG
TGGTTCTTCCTTAGGAACTGTGAAAACTTGAATGATTCTGTCAAAGTATTATGATGACATATTTTCTGATTCCGATTCTA
AGGATGAAGACCCAATAATATCGCAAGGAAGAAGAAAAAACAGCAACATCAGATTCCAGCCAATGGTGAGTGAATTATAT
GATCTTGAAAAAGACAGTAGAGATGAGGTCTTGGCGGATGCACAAAAAAGAAGAAACCATTGTTTTGAAGGGCACCTCTC
TCACCAACAACAGGCTGTTCCAAATGGTGATGTTGTCTTGTATTGC

Alignment

ORF - retro_mdom_1226 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 64.84 %
• Parental protein coverage: 62.68 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  SEDDDPYVVEEP-SDEEPALSSSEDEVDVLLHGTPDQKRKLIRECLTGESESSSEDEFEKE-MEAELNST
          SEDDDP.VV..P.S...P.LS.SE.EVDV.LHG.PDQK.K.IRECL.GESE...EDEFE...MEAELN.T
Retrocopy SEDDDP*VVKRP<SNRKPVLSCSEQEVDVFLHGAPDQKGKPIRECLPGESEPWCEDEFENK<MEAELNFT

Parental  IKTMEDKLSSIETGSSLGPVKTSVVLSKYYDDMYSDSDSEDEDTVISQ-VNKKKKKQQYRIPTNDE-LLY
          IKTME.KL...E.GSSLG.VKT...LSKYYDD..SDSDS.DED..ISQ...KKK...Q..IP.N.E..LY
Retrocopy IKTMEEKLTPLESGSSLGTVKT*MILSKYYDDIFSDSDSKDEDPIISQ<RKKKKQQHQ--IPANGE>ELY

Parental  DPEKDNRDQAWVDAQRRGYHCLGVQLSHQQQAVPNSDAVLNC
          D.EKD.RD....DAQ.R..HC....LSHQQQAVPN.D.VL.C
Retrocopy DLEKDSRDEVLADAQKRRNHCFEGHLSHQQQAVPNGDVVLYC

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	111.81 RPM
SRP007412_cerebellum	0.00 RPM	145.93 RPM
SRP007412_heart	0.00 RPM	49.24 RPM
SRP007412_kidney	0.00 RPM	136.95 RPM
SRP007412_liver	0.00 RPM	76.03 RPM
SRP007412_testis	0.00 RPM	228.85 RPM

ChIP-Seq

Monodelphis domestica was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mdom_1226 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_1226 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 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000005391	1 retrocopy	retro_cjac_3231,
Cavia porcellus	ENSCPOG00000003005	1 retrocopy	retro_cpor_898,
Myotis lucifugus	ENSMLUG00000013814	1 retrocopy	retro_mluc_596,
Monodelphis domestica	ENSMODG00000014525	1 retrocopy	retro_mdom_1226 ,
Mustela putorius furo	ENSMPUG00000001029	1 retrocopy	retro_mputfur_19,
Oryctolagus cuniculus	ENSOCUG00000003226	1 retrocopy	retro_ocun_1701,
Ictidomys tridecemlineatus	ENSSTOG00000005273	2 retrocopies	retro_itri_1598, retro_itri_237,
Tupaia belangeri	ENSTBEG00000001306	1 retrocopy	retro_tbel_4258,