RetrogeneDB ID: retro_mdom_262

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 3:478411645..478413031(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMODG00000023822
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSMODG00000014779
• Aliases: None
• Description: None

Sequence

>retro_mdom_262
ATGAACAGCTTTAGCAATGATGAATTTGACTTCAATTTCCTTGATGAAGGCTTTACTGCTAAGGATATTTTGGACCAGAA
AATTAATGAAGTTTCTTCTTCTGATGATAAAGATGCCTTCTATGTTGCTGACCTCGGTGACATCCTAAAGAAACATCTGA
GATGGTACAAAGCTCTTCCTCGAGTAACTCCTTTTTATGCTGTTAAATGTAATGACAGCAGAGCTATATTGAAGACACTT
GCTGCAGTAGGAGCAGGATTTGATTGTGCTAGCAAGACTGAAATACAATTAGTACAGAGTCTTGGGGTGCCACCAGGGAG
GATAATCTATGCAAATCCATGCAAACAAGTGTCACAAATTAAGTATGCTGCCAACAATGGAGTACAAATGATGACTTTTG
ATAGTGAAGTAGAGTTAATGAAAGTTGCCAGAGCTCATCCAAAGGCAAAGCTTGTTTTAAGTATTGCCACTGATGACTCC
AAAGCTGTCTGTCGTCTAAGTGTTAAATTTGGTGCCACTCTCAAAACTAGTAGGCTACTCCTTGAGCGGGCAAAGGAACT
GAATATTGATGTTATTGGAGTCAGTTTCCATGTGGGAAGTGGTTGTACTGATCCAGAAACATTTGTCCAAGCAGTCTCTG
ATGCTCGATGTGTCTTTGACATGGGGGCAGAGTTTGGTTTCAACATGTATCTTCTTGATATTGGTGGTGGCTTTCCTGGT
TCTGAAGATGTAAAGCTTAAATTTGAAGAGATCTCAAGTGTAATCAATCCAGCATTGGACAAGTATTTTCCTCCTGACTC
TGGAGTGCGAATCATAGCTGAACCTGGCAGATACTATGTTGCATCAGCTTTCACGCTTGCAGTTAACATCATTGCCAAAA
AACTTGTATTAAAAGAACAGACAGGCTCTGATGATGAAGATGAGGCAAATGACCAGACCTTTATGTACTATGTAAATGAT
GGAGTATATGGATCATTTAATTGTATCCTATTTGATCATGCACATGTTAAACCTCTTCTACAGAAGCGGCCCAAACCAGA
TGAGAAGTATTACTCTTCTAGCATATGGGGACCAACATGTGATGGCCTCGATCGAATTGTCGAACGCTGTGATTTACCAG
AAATGCATGTGGGAGATTGGATGCTGTTTGAAAACATGGGCGCTTATACTGTTGCTGCTGCTTCTACTTTCAATGGATTC
CAGAGACCCACTATCTATTATGTGATGTCTGGGCCAGCATGGCAATGCATGCAACAAATCAAGAACCAAGGCTTTCCAGC
AGAAGTAGAGGATCAGGATATCAACACTTTGCCATTGTCTTGTGCTTGGGAAAGTGGAATGGAACATCACTCAACAACTT
GTACTTCAGCTAGTGTTAATGTATAG

Alignment

ORF - retro_mdom_262 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 99.57 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MNSFSNDEFDFNFLDEGFTAKDILDQKINEVSSSDDKDAFYVADLGDILKKHLRWYKALPRVTPFYAVKC
          MNSFSNDEFDFNFLDEGFTAKDILDQKINEVSSSDDKDAFYVADLGDILKKHLRWYKALPRVTPFYAVKC
Retrocopy MNSFSNDEFDFNFLDEGFTAKDILDQKINEVSSSDDKDAFYVADLGDILKKHLRWYKALPRVTPFYAVKC

Parental  NDSRAILKTLAAVGAGFDCASKTEIQLVQSLGVPPERIIYANPCKQVSQIKYAANNGVQMMTFDSEVELM
          NDSRAILKTLAAVGAGFDCASKTEIQLVQSLGVPP.RIIYANPCKQVSQIKYAANNGVQMMTFDSEVELM
Retrocopy NDSRAILKTLAAVGAGFDCASKTEIQLVQSLGVPPGRIIYANPCKQVSQIKYAANNGVQMMTFDSEVELM

Parental  KVARAHPKAKLVLRIATDDSKAVCRLSVKFGATLKTSRLLLERAKELNIDVIGVSFHVGSGCTDPETFVQ
          KVARAHPKAKLVL.IATDDSKAVCRLSVKFGATLKTSRLLLERAKELNIDVIGVSFHVGSGCTDPETFVQ
Retrocopy KVARAHPKAKLVLSIATDDSKAVCRLSVKFGATLKTSRLLLERAKELNIDVIGVSFHVGSGCTDPETFVQ

Parental  AVSDARCVFDMGAEFGFNMYLLDIGGGFPGSEDVKLKFEEISSVINPALDKYFPPDSGVRIIAEPGRYYV
          AVSDARCVFDMGAEFGFNMYLLDIGGGFPGSEDVKLKFEEISSVINPALDKYFPPDSGVRIIAEPGRYYV
Retrocopy AVSDARCVFDMGAEFGFNMYLLDIGGGFPGSEDVKLKFEEISSVINPALDKYFPPDSGVRIIAEPGRYYV

Parental  ASAFTLAVNIIAKKLVLKEQTGSDDEDEANDQTFMYYVNDGVYGSFNCILFDHAHVKPLLQKRPKPDEKY
          ASAFTLAVNIIAKKLVLKEQTGSDDEDEANDQTFMYYVNDGVYGSFNCILFDHAHVKPLLQKRPKPDEKY
Retrocopy ASAFTLAVNIIAKKLVLKEQTGSDDEDEANDQTFMYYVNDGVYGSFNCILFDHAHVKPLLQKRPKPDEKY

Parental  YSSSIWGPTCDGLDRIVERCDLPEMHVGDWMLFENMGAYTVAAASTFNGFQRPTIYYVMSGPAWQCMQQI
          YSSSIWGPTCDGLDRIVERCDLPEMHVGDWMLFENMGAYTVAAASTFNGFQRPTIYYVMSGPAWQCMQQI
Retrocopy YSSSIWGPTCDGLDRIVERCDLPEMHVGDWMLFENMGAYTVAAASTFNGFQRPTIYYVMSGPAWQCMQQI

Parental  KNQGFPAEVEDQDINTLPLSCAWESGMEHHSTTCTSASVNV
          KNQGFPAEVEDQDINTLPLSCAWESGMEHHSTTCTSASVNV
Retrocopy KNQGFPAEVEDQDINTLPLSCAWESGMEHHSTTCTSASVNV

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	40.88 RPM
SRP007412_cerebellum	0.00 RPM	48.32 RPM
SRP007412_heart	0.00 RPM	30.50 RPM
SRP007412_kidney	0.00 RPM	111.93 RPM
SRP007412_liver	0.00 RPM	68.98 RPM
SRP007412_testis	0.00 RPM	424.49 RPM

ChIP-Seq

Monodelphis domestica was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mdom_262 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_262 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 16 parental genes, and 65 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000011415	1 retrocopy	retro_amel_414,
Bos taurus	ENSBTAG00000004256	1 retrocopy	retro_btau_552,
Choloepus hoffmanni	ENSCHOG00000010898	2 retrocopies	retro_chof_1618, retro_chof_2111,
Callithrix jacchus	ENSCJAG00000006576	2 retrocopies	retro_cjac_3170, retro_cjac_3857,
Dasypus novemcinctus	ENSDNOG00000018474	31 retrocopies	retro_dnov_1032, retro_dnov_1128, retro_dnov_1129, retro_dnov_1137, retro_dnov_1212, retro_dnov_1235, retro_dnov_1418, retro_dnov_1434, retro_dnov_1493, retro_dnov_1594, retro_dnov_1595, retro_dnov_1677, retro_dnov_1778, retro_dnov_1810, retro_dnov_1813, retro_dnov_2016, retro_dnov_2027, retro_dnov_2108, retro_dnov_2147, retro_dnov_2180, retro_dnov_2212, retro_dnov_2461, retro_dnov_2551, retro_dnov_2564, retro_dnov_392, retro_dnov_740, retro_dnov_766, retro_dnov_781, retro_dnov_923, retro_dnov_943, retro_dnov_958,
Equus caballus	ENSECAG00000022690	2 retrocopies	retro_ecab_1002, retro_ecab_957,
Loxodonta africana	ENSLAFG00000005330	2 retrocopies	retro_lafr_218, retro_lafr_850,
Myotis lucifugus	ENSMLUG00000010423	1 retrocopy	retro_mluc_281,
Macaca mulatta	ENSMMUG00000020441	2 retrocopies	retro_mmul_157, retro_mmul_1645,
Monodelphis domestica	ENSMODG00000014779	1 retrocopy	retro_mdom_262 ,
Mustela putorius furo	ENSMPUG00000013321	1 retrocopy	retro_mputfur_1272,
Mus musculus	ENSMUSG00000011179	12 retrocopies	retro_mmus_2588, retro_mmus_2744, retro_mmus_2745, retro_mmus_2746, retro_mmus_2747, retro_mmus_2834, retro_mmus_2922, retro_mmus_3237, retro_mmus_3677, retro_mmus_503, retro_mmus_912, retro_mmus_984,
Nomascus leucogenys	ENSNLEG00000013820	1 retrocopy	retro_nleu_1119,
Pongo abelii	ENSPPYG00000012654	1 retrocopy	retro_pabe_3090,
Ictidomys tridecemlineatus	ENSSTOG00000000386	2 retrocopies	retro_itri_1751, retro_itri_801,
Tursiops truncatus	ENSTTRG00000004611	3 retrocopies	retro_ttru_1940, retro_ttru_731, retro_ttru_843,