RetrogeneDB ID: retro_mdom_223

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 1:13071639..13074216(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMODG00000025340
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: EEF2
• Ensembl ID: ENSMODG00000000750
• Aliases: None
• Description: elongation factor 2 [Source:RefSeq peptide;Acc:NP_001239532]

Sequence

>retro_mdom_223
ATGGTGAACTTTACAGTAGACCAGATCCGGGCCATCATGGACAAAAAGGCCAATATCAGAAACATGTCTGTAATAGCTCA
TGTGGATCATGGCAAGTCAACCCTGACGGATTCCCTGGTTTGCAAAGCTGGTATTATTGCTTCAGCCCGTGCTGGTGAGA
CCAGGTTCACTGACACGAGAAAAGATGAACAGGAACGGTGCATCACTATTAAGTCAACTGCCATTTCCCTCTTTTATGAG
CTGTCAGAAAATGATTTGAACTTCATCAAGCAGAGCAAAGATGGTTCTGGCTTTCTTATCAACCTCATTGACTCACCTGG
GCACGTTGACTTCTCATCAGAAGTAACAGCTGCACTCCGTGTTACTGATGGTGCCTTGGTTGTGGTGGATTGTGTATCTG
GTGTATGTGTTCAGACTGAGACTGTACTTCGCCAGGCCATTGCTGAAAGAATCAAGCCTGTTTTGATGATGAACAAGATG
GACCGGGCCTTACTTGAACTCCAGCTGGAGCCTGAGGAACTGTATCAGACATTTCAGCGAATTGTAGAGAATGTGAATGT
CATCATCTCCACCTATGGAGAGGGAGAAAGTGGCCCTATGGGAAACATCATGATTGATCCTGTCCTTGGTACTGTTGGGT
TTGGTTCTGGACTTCATGGTTGGGCCTTTACTCTGAAGCAGTTTGCAGAGATGTATGTGGCAAAATTTGCAGCCAAGGGT
GAAGGTCAGCTGGGACCAGCTGAAAGGGCCAAGAAAGTAGAGGACATGATGAAAAAACTTTGGGGTGACCGGTATTTTGA
TCCTACCAATGGGAAGTTTAGCAAATCTGCTACTAGCCCTGATGGAAAGAAGTTGCCTAGAACTTTCTGCCAACTCATCT
TAGATCCAATCTTCAAGGTATTTGATGCAATTATGACCTTTAAGAAGGAGGAAACTGCAAAACTGATTGAAAAACTTGAC
ATCAAATTGGACAGTGAAGATAAAGACAAAGAGGGAAAACCACTTCTAAAGGCTGTGATGAGACGTTGGCTGCCTGCTGG
AGATGCACTTCTCCAAATGATAACCATCCACCTGCCTTCCCCTGTAACTGCTCAGAAATACCGTTGTGAACTGTTATATG
AGGGTCCCCCTGATGATGAGGCTGCTATGGGTATTAAAAGCTGTGATCCCAAGGGTCCCCTGATGATGTACATCTCAAAA
ATGGTGCCAACCTCTGACAAAGGCAGATTCTATGCTTTTGGCCGTGTATTTTCTGGTCTTGTTTCCACTGGCCTAAAAGT
CAGAATCATGGGACCCAATTATACCCCTGGGAAGAAGGAAGATCTCTACCTGAAGCCAATTCAAAGGACAATTCTGATGA
TGGGCCGATATGTTGAACCTATTGAAGATGTGCCTTGTGGTAACATTGTTGGTCTGGTTGGTGTGGATCAGTTCCTTGTG
AAAACGGGTACCATTACTACCTTTGAGCATGCCCACAACATGAGGGTGATGAAGTTTAGCGTTAGCCCCGTGGTGCGAGT
AGCTGTTGAAGCAAAGAACCCAGCTGACCTGCCCAAACTTGTGGAAGGATTGAAGCGTTTGGCCAAGTCTGACCCTATGG
TCCAGTGTATCATTGAGGAATCTGGAGAACACATTATTGCTGGTGCAGGGGAGTTGCATCTGGAGATCTGCCTGAAAGAT
CTTGAAGAAGATCATGCCTGCATTCCCATCAAGAAATCGGACCCTGTTGTCTCCTACCGTGAGACAGTCAGTGAGGAGTC
AAATGTTCTCTGCCTTTCCAAATCTCCCAATAAGCACAACAGGCTATACATGAAGGCTCGGCCATTCCCTGATGGCCTGG
CTGAAGATATTGACAAAGGTGAAGTCTCAGCTCGCCAGGAGCTCAAACAAAGGGCTCGATATCTGGCTGAGAAGTACGAG
TGGGATGTGACTGAAGCCCGTAAGATCTGGTGCTTTGGCCCTGATGGAACTGGGCCCAATGTTCTTACTGATATCACCAA
GGGAGTACAGTACCTTAATGAGATCAAGGACAGCGTAGTGGCTGGATTTCAGTGGGCTACCAAGGAGGGAGCACTGTGTG
AGGAGAACATGCGGGCAGTCCGTTTTGATGTACATGATGTGACCCTGCATGCTGACGCCATTCACCGTGGTGGTGGTCAA
ATCATTCCCACAGCCCGGCGTTGCCTATATGCCTGCGTACTGACTGCCCAGCCTCGTCTTATGGAACCTATCTATCTTGT
GGAGATTCAGTGTCCAGAACAAGTGGTTGGTGGCATTTATGGTGTCCTGAACAGGAAGCGAGGGCATGTGTTTGAGGAGT
CCCAGGTTGCTGGCACCCCTATGTTTGTTGTGAAAGCCTATCTGCCTGTCAATGAATCTTTTGGCTTCACAGCTGACTTG
AGGTCTAATACAGGTGGCCAAGCCTTCCCTCAGTGTGTATTTGACCATTGGCAGATCCTTCCTGGAGACCCTTTTGACAG
TACTAGCCGCCCTTGCCAGGTTGTGGCAGATACCCGCAAACGTAAAGGGCTGAAGGAAGGTATCCCAGCCCTGGACAACT
TCCTGGACAAGTTGTAA

Alignment

ORF - retro_mdom_223 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 99.18 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  VNFTVDQIRAIMDKKANIRNMSVIAHVDHGKSTLTDSLVCKAGIIASARAGETRFTDTRKDEQERCITIK
          VNFTVDQIRAIMDKKANIRNMSVIAHVDHGKSTLTDSLVCKAGIIASARAGETRFTDTRKDEQERCITIK
Retrocopy VNFTVDQIRAIMDKKANIRNMSVIAHVDHGKSTLTDSLVCKAGIIASARAGETRFTDTRKDEQERCITIK

Parental  STAISLFYELSENDLNFIKQSKDGSGFLINLIDSPGHVDFSSEVTAALRVTDGALVVVDCVSGVCVQTET
          STAISLFYELSENDLNFIKQSKDGSGFLINLIDSPGHVDFSSEVTAALRVTDGALVVVDCVSGVCVQTET
Retrocopy STAISLFYELSENDLNFIKQSKDGSGFLINLIDSPGHVDFSSEVTAALRVTDGALVVVDCVSGVCVQTET

Parental  VLRQAIAERIKPVLMMNKMDRALLELQLEPEELYQTFQRIVENVNVIISTYGEGESGPMGNIMIDPVLGT
          VLRQAIAERIKPVLMMNKMDRALLELQLEPEELYQTFQRIVENVNVIISTYGEGESGPMGNIMIDPVLGT
Retrocopy VLRQAIAERIKPVLMMNKMDRALLELQLEPEELYQTFQRIVENVNVIISTYGEGESGPMGNIMIDPVLGT

Parental  VGFGSGLHGWAFTLKQFAEMYVAKFAAKGEGQLGPAERAKKVEDMMKKLWGDRYFDPTNGKFSKSATSPD
          VGFGSGLHGWAFTLKQFAEMYVAKFAAKGEGQLGPAERAKKVEDMMKKLWGDRYFDPTNGKFSKSATSPD
Retrocopy VGFGSGLHGWAFTLKQFAEMYVAKFAAKGEGQLGPAERAKKVEDMMKKLWGDRYFDPTNGKFSKSATSPD

Parental  GKKLPRTFCQLILDPIFKVFDAIMTFKKEETAKLIEKLDIKLDSEDKDKEGKPLLKAVMRRWLPAGDALL
          GKKLPRTFCQLILDPIFKVFDAIMTFKKEETAKLIEKLDIKLDSEDKDKEGKPLLKAVMRRWLPAGDALL
Retrocopy GKKLPRTFCQLILDPIFKVFDAIMTFKKEETAKLIEKLDIKLDSEDKDKEGKPLLKAVMRRWLPAGDALL

Parental  QMITIHLPSPVTAQKYRCELLYEGPPDDEAAMGIKSCDPKGPLMMYISKMVPTSDKGRFYAFGRVFSGLV
          QMITIHLPSPVTAQKYRCELLYEGPPDDEAAMGIKSCDPKGPLMMYISKMVPTSDKGRFYAFGRVFSGLV
Retrocopy QMITIHLPSPVTAQKYRCELLYEGPPDDEAAMGIKSCDPKGPLMMYISKMVPTSDKGRFYAFGRVFSGLV

Parental  STGLKVRIMGPNYTPGKKEDLYLKPIQRTILMMGRYVEPIEDVPCGNIVGLVGVDQFLVKTGTITTFEHA
          STGLKVRIMGPNYTPGKKEDLYLKPIQRTILMMGRYVEPIEDVPCGNIVGLVGVDQFLVKTGTITTFEHA
Retrocopy STGLKVRIMGPNYTPGKKEDLYLKPIQRTILMMGRYVEPIEDVPCGNIVGLVGVDQFLVKTGTITTFEHA

Parental  HNMRVMKFSVSPVVRVAVEAKNPADLPKLVEGLKRLAKSDPMVQCIIEESGEHIIAGAGELHLEICLKDL
          HNMRVMKFSVSPVVRVAVEAKNPADLPKLVEGLKRLAKSDPMVQCIIEESGEHIIAGAGELHLEICLKDL
Retrocopy HNMRVMKFSVSPVVRVAVEAKNPADLPKLVEGLKRLAKSDPMVQCIIEESGEHIIAGAGELHLEICLKDL

Parental  EEDHACIPIKKSDPVVSYRETVSEESNVLCLSKSPNKHNRLYMKARPFPDGLAEDIDKGEVSARQELKQR
          EEDHACIPIKKSDPVVSYRETVSEESNVLCLSKSPNKHNRLYMKARPFPDGLAEDIDKGEVSARQELKQR
Retrocopy EEDHACIPIKKSDPVVSYRETVSEESNVLCLSKSPNKHNRLYMKARPFPDGLAEDIDKGEVSARQELKQR

Parental  ARYLAEKYEWDVTEARKIWCFGPDGTGPNVLTDITKGVQYLNEIKDSVVAGFQWATKEGALCEENMRAVR
          ARYLAEKYEWDVTEARKIWCFGPDGTGPNVLTDITKGVQYLNEIKDSVVAGFQWATKEGALCEENMRAVR
Retrocopy ARYLAEKYEWDVTEARKIWCFGPDGTGPNVLTDITKGVQYLNEIKDSVVAGFQWATKEGALCEENMRAVR

Parental  FDVHDVTLHADAIHRGGGQIIPTARRCLYACVLTAQPRLMEPIYLVEIQCPEQVVGGIYGVLNRKRGHVF
          FDVHDVTLHADAIHRGGGQIIPTARRCLYACVLTAQPRLMEPIYLVEIQCPEQVVGGIYGVLNRKRGHVF
Retrocopy FDVHDVTLHADAIHRGGGQIIPTARRCLYACVLTAQPRLMEPIYLVEIQCPEQVVGGIYGVLNRKRGHVF

Parental  EESQVAGTPMFVVKAYLPVNESFGFTAELRANTGGQAFPQWVFEHWEILPGEPFDSTNRPCQVVADTRKR
          EESQVAGTPMFVVKAYLPVNESFGFTA.LR.NTGGQAFPQ.VF.HW.ILPG.PFDST.RPCQVVADTRKR
Retrocopy EESQVAGTPMFVVKAYLPVNESFGFTADLRSNTGGQAFPQCVFDHWQILPGDPFDSTSRPCQVVADTRKR

Parental  KGLKEGIPALDNFLDKL
          KGLKEGIPALDNFLDKL
Retrocopy KGLKEGIPALDNFLDKL

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	408.85 RPM	0.00 RPM
SRP007412_cerebellum	488.05 RPM	0.00 RPM
SRP007412_heart	995.96 RPM	0.00 RPM
SRP007412_kidney	1219.39 RPM	0.00 RPM
SRP007412_liver	1200.82 RPM	0.00 RPM
SRP007412_testis	419.19 RPM	0.00 RPM

ChIP-Seq

Monodelphis domestica was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mdom_223 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_223 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 6 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000004258	2 retrocopies	retro_btau_1809, retro_btau_539,
Canis familiaris	ENSCAFG00000019158	1 retrocopy	retro_cfam_1503,
Latimeria chalumnae	ENSLACG00000011124	1 retrocopy	retro_lcha_83,
Macaca mulatta	ENSMMUG00000022767	1 retrocopy	retro_mmul_2026,
Monodelphis domestica	ENSMODG00000000750	1 retrocopy	retro_mdom_223 ,
Mus musculus	ENSMUSG00000034994	1 retrocopy	retro_mmus_2521,