RetrogeneDB ID: retro_mdom_1243

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 4:65117872..65118472(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: EIF3H
• Ensembl ID: ENSMODG00000004154
• Aliases: None
• Description: eukaryotic translation initiation factor 3, subunit H [Source:HGNC Symbol;Acc:3273]

Sequence

>retro_mdom_1243
GATCCCATAAAAACTATTCAAGTGTCTCTATCATTGAAGGCATATAGGCTAACTCCTAAGCTGATGGAAGTTTGTAAAGA
GAAAGATTTTTCTCCAGAAGCATTGAAAAAGGCAAATATCACTTTTGAGCACATGTTTGAAGAAGTGCAGATTATAATTA
AAAATTCACATTTGATCAATGTACTAATGTGGGAACTAGAAAAGAAATCAGCTGTGGCAGATAAACATGAATTGTTCAGT
CTAGCCAGCAATAATCACCTGGGAAAGAGTCTGCAATTATTGATGGACAGAGTGGATGAAATGAGTCAGGATATAGTTAA
ATATAACACCTATATGAGAAACACCAGTAAATAGCAGCAACAGAAACATCAGTATCAGCAGTGGCATCAGCAGGAGAATC
AGCAGCTCCAGAGCCGAGGAGAACCACCTCTTCCTGAAGAAGACATGTCCAAACTCTTCAAACCTCTTCAGCCACCAGCT
AGGATGGATTCACTGCTTATTGCAGGCCAAATTAATACTTACTGCCAGAACATCAAAGAATTCACTGCACAGAATTTGGG
CAAACTCTTCATGGCTCAAGCTCTTCAAGAATATAACAAC

Alignment

ORF - retro_mdom_1243 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 88. %
• Parental protein coverage: 56.66 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  DPIKTAQGSLSLKAYRLTPKLMEVCKEKDFSPEALKKANITFEHMFEEVPIIIKNSHLINVLMWELEKKS
          DPIKT.Q.SLSLKAYRLTPKLMEVCKEKDFSPEALKKANITFEHMFEEV.IIIKNSHLINVLMWELEKKS
Retrocopy DPIKTIQVSLSLKAYRLTPKLMEVCKEKDFSPEALKKANITFEHMFEEVQIIIKNSHLINVLMWELEKKS

Parental  AVADKHELLSLASSNHLGKSLQLLMDRVDEMSQDIVKYNTYMRNTSKQQQQKHQYQQRRQQENQQRQSRG
          AVADKHEL.SLAS.NHLGKSLQLLMDRVDEMSQDIVKYNTYMRNTSK...................QSRG
Retrocopy AVADKHELFSLASNNHLGKSLQLLMDRVDEMSQDIVKYNTYMRNTSKXXXXXXXXXXXXXXXXXXXQSRG

Parental  EPPLPEEDMSKLFKPLQPPARMDSLLIAGQINTYCQNIKEFTAQNLGKLFMAQALQEYNN
          EPPLPEEDMSKLFKPLQPPARMDSLLIAGQINTYCQNIKEFTAQNLGKLFMAQALQEYNN
Retrocopy EPPLPEEDMSKLFKPLQPPARMDSLLIAGQINTYCQNIKEFTAQNLGKLFMAQALQEYNN

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_1243 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_1243 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 14 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000000816	1 retrocopy	retro_cfam_2073,
Callithrix jacchus	ENSCJAG00000005910	1 retrocopy	retro_cjac_3023,
Echinops telfairi	ENSETEG00000000324	1 retrocopy	retro_etel_24,
Macropus eugenii	ENSMEUG00000015663	4 retrocopies	retro_meug_1223, retro_meug_1244, retro_meug_1790, retro_meug_376,
Monodelphis domestica	ENSMODG00000004154	1 retrocopy	retro_mdom_1243 ,
Mus musculus	ENSMUSG00000022312	1 retrocopy	retro_mmus_1668,
Oryctolagus cuniculus	ENSOCUG00000007534	1 retrocopy	retro_ocun_608,
Otolemur garnettii	ENSOGAG00000008905	1 retrocopy	retro_ogar_2043,
Sorex araneus	ENSSARG00000009067	1 retrocopy	retro_sara_69,
Sarcophilus harrisii	ENSSHAG00000014977	1 retrocopy	retro_shar_561,
Ictidomys tridecemlineatus	ENSSTOG00000001403	1 retrocopy	retro_itri_420,