RetrogeneDB ID: retro_mdom_395

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 1:382188820..382189244(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RPS23
• Ensembl ID: ENSMODG00000020255
• Aliases: None
• Description: ribosomal protein S23 [Source:HGNC Symbol;Acc:10410]

Sequence

>retro_mdom_395
ATAGGTAAGTGCCATGGTCTTTGTACCCAGTAGAAGGCTCTTCACCACAGCTACAGGAGAGACCAAAATTGGCATGACAA
ATAGTACAAGAAAGCTGCACTAAAGGCCATTCCATTTAGAGGAAAATCTAATGCAAAAGGAATTGTCTTGGGAAAAGTTG
GTGTGGAAGCCATGCAGCCCAATTCTGCCATCCAGAAGTATGTGAGAATTCAGCTAATTAAAGATGACAAAAAAATCCAC
TGTCTTTGTTCCCAAGGCTCTCAACTTCAATTTTGTTGAGGAAAATGATGTAGTTTTGGTTGCTGGATTTGGTCAGGAAA
AAAGTCATGCTGTTGGTGATATTCCTAGAGTCTGTTTCAAGGTTGTAAAAGTTGAAAACATTTCTCTTCTGGCCTCGTAC
AAAGGCAAGAAGGAAAGACCAAGG

Alignment

ORF - retro_mdom_395 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 69.86 %
• Parental protein coverage: 99.3 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MGKCRGLRTARKL--RSHRRDQKWHDKQYKKAHLGTALKANPFGGASHAKGIVLEKVGVEAKQPNSAIRK
          .GKC.GL.T..K....S.RRDQ.WHDK.YKKA....ALKA.PF.G.S.AKGIVL.KVGVEA.QPNSAI.K
Retrocopy IGKCHGLCTQ*KALHHSYRRDQNWHDK*YKKA----ALKAIPFRGKSNAKGIVLGKVGVEAMQPNSAIQK

Parental  CVRVQLIKNGKKI-TAFVPNDGCLNFIEENDEVLVAGFGR-KGHAVGDIPGVRFKVVKVANVSLLALYKG
          .VR.QLIK..KKI.T.FVP.....NF.EEND.VLVAGFG..K.HAVGDIP.V.FKVVKV.N.SLLA.YKG
Retrocopy YVRIQLIKDDKKI>TVFVPKALNFNFVEENDVVLVAGFGQEKSHAVGDIPRVCFKVVKVENISLLASYKG

Parental  KKERPR
          KKERPR
Retrocopy KKERPR

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	0.12 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_395 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_395 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 12 parental genes, and 45 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000013358	3 retrocopies	retro_btau_173, retro_btau_205, retro_btau_80,
Callithrix jacchus	ENSCJAG00000011247	2 retrocopies	retro_cjac_126, retro_cjac_256,
Homo sapiens	ENSG00000186468	6 retrocopies	retro_hsap_1778, retro_hsap_2940, retro_hsap_3107, retro_hsap_3287, retro_hsap_3989, retro_hsap_4697,
Gorilla gorilla	ENSGGOG00000025014	6 retrocopies	retro_ggor_1316, retro_ggor_2038, retro_ggor_2131, retro_ggor_2237, retro_ggor_2677, retro_ggor_286,
Macaca mulatta	ENSMMUG00000003578	4 retrocopies	retro_mmul_1239, retro_mmul_1974, retro_mmul_2305, retro_mmul_852,
Monodelphis domestica	ENSMODG00000020255	3 retrocopies	retro_mdom_1518, retro_mdom_1612, retro_mdom_395 ,
Mustela putorius furo	ENSMPUG00000008114	1 retrocopy	retro_mputfur_1298,
Nomascus leucogenys	ENSNLEG00000013203	3 retrocopies	retro_nleu_1353, retro_nleu_1909, retro_nleu_764,
Oryctolagus cuniculus	ENSOCUG00000010363	2 retrocopies	retro_ocun_195, retro_ocun_95,
Rattus norvegicus	ENSRNOG00000016580	12 retrocopies	retro_rnor_100, retro_rnor_1394, retro_rnor_149, retro_rnor_1691, retro_rnor_1941, retro_rnor_1959, retro_rnor_1982, retro_rnor_2119, retro_rnor_2182, retro_rnor_2492, retro_rnor_525, retro_rnor_559,
Sarcophilus harrisii	ENSSHAG00000008347	2 retrocopies	retro_shar_257, retro_shar_348,
Sus scrofa	ENSSSCG00000014133	1 retrocopy	retro_sscr_92,