RetrogeneDB ID: retro_mdom_86

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 3:143751663..143752635(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMODG00000005318
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: SEPHS1
• Ensembl ID: ENSMODG00000016864
• Aliases: None
• Description: selenophosphate synthetase 1 [Source:HGNC Symbol;Acc:19685]

Sequence

>retro_mdom_86
ATGGACTCCTGCGTGATCCCCTTGAGACATGGAGGACTTTCGCTTGTGCAGACCACTGACTTCTTTTACCCTTTGGTTGA
AGACCCCTACATGATGGGACGAATTGCCTGCGCCAATGTGCTAAGTGATCTTTATGCCATGGGCATTACCGAATGTGATA
ACATGCTGATGTTACTTAGTGTCAGCCAAAAGATGAATGAGGAGGAGAGAGAAAAAGTAATGCCTCTCATGATCAAAGGC
TTTAGAGATGCTGCTGAGGAAGGAGGAACCTCTGTGACCGGGGGACAGACCGTGGTAAATCCCTGGATCATAATTGGAGG
TGTTGCTACTGTGGTCTGTCAACCTAATGAATTCATCATGCCAGACAGTGCGGTTCCTGGGGACGTGCTGGTATTGACCA
AACCCTTAGGAACTCAAGTGGCAGTCAATGCCCACCAGTGGCTGGATAATCCAGAAAAGTGGAATAAAATAAAATTAGTG
GTAACCAGAGAAGATGTAGAGTTGGCCTATCAGGAAGCTATGTTTAGTATGGCCATGCTGAATAGAACTGCTGCTGGATT
AATGCACACCTTTAATGCTCATGCTGCCACTGATGTCACTGGCTTTGGAATCTTGGGACATGCTCAGAATCTTGCAAAGC
AACAAAGAAGTCAAGTATCCTTTGTCATTCATAATCTACCAATCATTGCCAAGATGGCTGCTATTAGTAAGGCCAGTGGG
CGTTTTGGTCTTCTCCAGGGAACATCAGCGGAAACCTCTGGGGGTCTACTGATTTGTCTGCCCCGAGAACATGCAGCTCG
CTTTTGTGCTGAAATTAAGTCTCCCAAATATGGAGAGGGTCACCAAGCATGGATTATTGGCATCGTGGAAAAAGGAAACC
AGACAGCCCGCATCATCGACAAACCAGGGATTATCGAAGTCACACCTCGTGGAGCCACTGTACCCCTTCATCCCAATAAT
TCCCATGCTAGC

Alignment

ORF - retro_mdom_86 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 83.39 %
• Parental protein coverage: 81.38 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MDTCVIPLRHGGLSLVQTTDYIYPIVDDPYMMGRIACANVLSDLYAMGVTECDNMLMLLGISNKMTDRER
          MD.CVIPLRHGGLSLVQTTD..YP.V.DPYMMGRIACANVLSDLYAMG.TECDNMLMLL..S.KM...ER
Retrocopy MDSCVIPLRHGGLSLVQTTDFFYPLVEDPYMMGRIACANVLSDLYAMGITECDNMLMLLSVSQKMNEEER

Parental  DKVVPLIIQGFKDAAEEAGTSVTGGQTVLNPWIVLGGVATTVCQPNEFIMPDNAVPGDVLVLTKPLGTQV
          .KV.PL.I.GF.DAAEE.GTSVTGGQTV.NPWI..GGVAT.VCQPNEFIMPD.AVPGDVLVLTKPLGTQV
Retrocopy EKVMPLMIKGFRDAAEEGGTSVTGGQTVVNPWIIIGGVATVVCQPNEFIMPDSAVPGDVLVLTKPLGTQV

Parental  AVAVHQWLDIPEKWNKIKLVVTQEDVELAYQEAMMNMARLNRTAAGLMHTFNAHAATDITGFGILGHAQN
          AV..HQWLD.PEKWNKIKLVVT.EDVELAYQEAM..MA.LNRTAAGLMHTFNAHAATD.TGFGILGHAQN
Retrocopy AVNAHQWLDNPEKWNKIKLVVTREDVELAYQEAMFSMAMLNRTAAGLMHTFNAHAATDVTGFGILGHAQN

Parental  LAKQQRNEVSFVIHNLPVLAKMAAVSKACGNMFGLMHGTCPETSGGLLICLPREQAARFCAEIKSPKYGE
          LAKQQR..VSFVIHNLP..AKMAA.SKA.G..FGL..GT..ETSGGLLICLPRE.AARFCAEIKSPKYGE
Retrocopy LAKQQRSQVSFVIHNLPIIAKMAAISKASGR-FGLLQGTSAETSGGLLICLPREHAARFCAEIKSPKYGE

Parental  GHQAWIIGIVEKGNRTARIIDKPRIIEVAPQVATQNVNP
          GHQAWIIGIVEKGN.TARIIDKP.IIEV.P..AT....P
Retrocopy GHQAWIIGIVEKGNQTARIIDKPGIIEVTPRGATVPLHP

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_86 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_86 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 21 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000009494	2 retrocopies	retro_cjac_166, retro_cjac_2219,
Gorilla gorilla	ENSGGOG00000003806	2 retrocopies	retro_ggor_147, retro_ggor_2924,
Myotis lucifugus	ENSMLUG00000001971	2 retrocopies	retro_mluc_2350, retro_mluc_728,
Macaca mulatta	ENSMMUG00000021233	4 retrocopies	retro_mmul_1607, retro_mmul_2495, retro_mmul_2647, retro_mmul_922,
Monodelphis domestica	ENSMODG00000016864	1 retrocopy	retro_mdom_86 ,
Nomascus leucogenys	ENSNLEG00000012205	7 retrocopies	retro_nleu_1868, retro_nleu_2211, retro_nleu_234, retro_nleu_2668, retro_nleu_2873, retro_nleu_3004, retro_nleu_327,
Pteropus vampyrus	ENSPVAG00000002945	2 retrocopies	retro_pvam_115, retro_pvam_566,
Rattus norvegicus	ENSRNOG00000018125	1 retrocopy	retro_rnor_59,