RetrogeneDB ID: retro_mdom_279

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 1:576318899..576320768(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMODG00000010492
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSMODG00000008679
• Aliases: None
• Description: None

Sequence

>retro_mdom_279
ATGGCGTCCACGGACTATAGTACCTACAGTCAAGCTGCAGCCCAGCAGGACTACAGTGCTTATGCAGCCCAGCCAGCTCA
AGGATATGCACAGACCACCCAGGCATGTGGGCAACAAAGTTATGGAGACTATGAGCAGCCTACTGATGTCAGCTATACAC
AGGCTCAAACAACTGCGATGTATGGGCAGACTGCGTATGCAACCTCTTATGGACAGCCTCCAACAGGTTATACTACACCA
ACCTCACCTCAGGCTTACAGTCAGCCTGTCCAAGAATATGGCCCGGGGGCCTACGATACCACCACTGCTACAGTTACGAC
CACCCAAGCATCCTATGCAGCCCAATCTGCATATGGCACCCAGCCTGCTTACCCAACCTATGGGCAGCAGCCAGCAAGAC
CCCAGGATGGTAGCAAGCCCGCTGAGACTAGTCAGCCTCAATCTAGTACAGCAGGCTACAGCCAACCCAGCCTAGGATAC
GGGCAGAGCAACTACAGTTACCCACAGGGGCCCGGCAGCGACCCCAGGCAGCCAGTCACCGCACCTCCTTCCTATCCTCC
AACCAGCTATTCCTCTACGCAGCCGACTAGTTACGATGAGAGCAGTTACTCCCAGCAGAATACCTATGGGCAGCAGAGCA
TTTATGGACAGCAGAGTGGCTATGGTCAACAGCCCCCCACGAGTGGGCCCCCCCAAACTGGATCCTACAGCCAGGCTCCA
AGTCAATCTAGCCAACAGAGCAGCAGCTACGGGCAGCAGAGTGCCTTCCAGCAGGACCATCCCAGTAGCATGGGTGTATA
TGGGCAGGAGTCTGGAGGCTTTTCCGGATCTGGAGAAAACCAGAGCATGAGTGGCCCTGATGACCCGGGCAGGGGAAGAG
GGGGATTTGATTGTGGAGGCATGAGCAGAGGTGGGCGGGGAGGAGGGGGAGGAGGACACGGTGGAATGGGCAGCGCTGGA
GAGCGAGGTGGCTTCAGTAAGCCTGGTGGACCTATGGAAGAAGCACCAGACCTTGACTTGGGCCCACCTGTAGATCCAGA
TGAAGACCCTGAAAACAGTGCAATTTATGTACAGGGCCTGAACGAAAGCGTGACTGCTGATGAGCTGGCAGACTTTTTCA
AACAGTGTGGGGTTGTCAAGATGAACAAAAGGACTGGGCAGCCGGTGATTAACATTTACTTAGACAAGGAAACCGGGAAA
CCCAAAGGAGATGCCACCGTGTCCTATGATGACCCACCTACTGCAAAGGCTGCAGTAGAATGGTTTGATGGGAAAGATTT
CCAAGGGAGCAAACTCAAAGTGTCTCTTGCTCGAGGTGGTATGCCACCCCGTGAAGGCAGAGGGATGCCTCCCCCTCTCC
GAGGAGGTCCTGAAGGACCAGGGGGGCCAGGAGGTCCCATGGGTCGAATGGGAGGCAGAGGAGGAGACAGGGAAGGTTTT
CCACCAAGAGGACCCAGGGGTTCCCGTGGAAACCCCTCAGGAGGAGAAAATGTCCAGCACAGAGCAGGGGATTGGCAGTG
CCCTAATCCAGGCTGCGGAAACCAGAATTTTGCCTGGAGAACAGAGTGTAATCAATGCAAGGCCCCTAAGCCAGAGGGCA
GAGGTGGCCCCGGTGGCATGAGGAGTGGCAGAGGTGGGCTCATGGACCATGGTGGGCCTGGCGGTATGTTCCGAGGAGGC
CGAGGTGGAGACAGAGGCGACTTTCGGGGAGGTCGAGGCATGGACCAAGGGGACTTTGGTGGAGGAAGAAGAAGAGGCCC
TGGGGGTCCTCCCAGACCTCTCATGGAGCAAATGGGTGGCAGAAGAGGAGGGCATGGCAGGCCTGGAAAAGGTGAGCGTC
GCCAGGAGCGCAGAGACCGGCCCTACTAG

Alignment

ORF - retro_mdom_279 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 72.44 %
• Parental protein coverage: 67.32 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  TTTQASYAAQSAYGTQPAYPTYGQQPATAAPARPQDGSKPAETSQPQSSTAGYSQPSLGYGQSNYSYPQV
          TTT......Q..Y..Q.A...YG.QP..A.P...Q....P...S.P.......S....GY.Q....Y.Q.
Retrocopy TTTATVTTTQASYAAQSA---YGTQP--AYPTYGQQPARPQDGSKPAETSQPQSSTA-GYSQPSLGYGQS

Parental  PGSYPMQPVTAP--PSYPPTSYSSTQPTSYDQSSYSQQNTYGQQSSYGQQSSYGQQSSYGQQPPTSYPPQ
          ..SYP..P...P..P...P.SY..T...S....SY.....Y.QQ..YGQQS.YGQQS.YGQQPPTS.PPQ
Retrocopy NYSYPQGPGSDPRQPVTAPPSYPPTSYSSTQPTSYDE-SSYSQQNTYGQQSIYGQQSGYGQQPPTSGPPQ

Parental  TGSYSQAPSQYSQQSSSYGQQSAFRQDHPSSMGVYGQESGGFSGPGENRSMSGPDNRGRGRGGFDRGGMS
          TGSYSQAPSQ.SQQSSSYGQQSAF.QDHPSSMGVYGQESGGFSG.GEN.SMSGPD..GRGRGGFD.GGMS
Retrocopy TGSYSQAPSQSSQQSSSYGQQSAFQQDHPSSMGVYGQESGGFSGSGENQSMSGPDDPGRGRGGFDCGGMS

Parental  RGGRGGGGGGRGGMG-AGERGGFNKPGGPMEEGPDLDLGSPVDPDEDSENSAIYVQGLNESVTADELADF
          RGGRGGGGGG.GGMG.AGERGGF.KPGGPMEE.PDLDLG.PVDPDED.ENSAIYVQGLNESVTADELADF
Retrocopy RGGRGGGGGGHGGMGSAGERGGFSKPGGPMEEAPDLDLGPPVDPDEDPENSAIYVQGLNESVTADELADF

Parental  FKQCGVVKMNKRTGQPMINIYLDKETGKPKGDATVSYDDPPTAKAAVEWFDGKDFQGSKLKVSLARKKPP
          FKQCGVVKMNKRTGQP.INIYLDKETGKPKGDATVSYDDPPTAKAAVEWFDGKDFQGSKLKVSLAR...P
Retrocopy FKQCGVVKMNKRTGQPVINIYLDKETGKPKGDATVSYDDPPTAKAAVEWFDGKDFQGSKLKVSLARGGMP

Parental  MNSMRGGMPPREGRGMPPPLRGGPGGPGGPGGPMGRMGGRGGDRGGFPPRGPRGSRGNPSGGGNVQHRAG
          ....RG..PP..G....P...GGPGGP.G....MG..GG...DR.GFPPRGPRGSRGNPSGG.NVQHRAG
Retrocopy PREGRGMPPPLRGGPEGP---GGPGGPMG---RMGGRGG---DREGFPPRGPRGSRGNPSGGENVQHRAG

Parental  DWQCPNPGCGNQNFAWRTECNQCKAPKPEG
          DWQCPNPGCGNQNFAWRTECNQCKAPKPEG
Retrocopy DWQCPNPGCGNQNFAWRTECNQCKAPKPEG

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	7.03 RPM	0.00 RPM
SRP007412_cerebellum	9.14 RPM	0.00 RPM
SRP007412_heart	5.18 RPM	0.00 RPM
SRP007412_kidney	0.00 RPM	0.00 RPM
SRP007412_liver	4.53 RPM	0.00 RPM
SRP007412_testis	11.00 RPM	0.00 RPM

ChIP-Seq

Monodelphis domestica was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mdom_279 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_279 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 17 parental genes, and 30 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000008298	2 retrocopies	retro_amel_191, retro_amel_959,
Canis familiaris	ENSCAFG00000012160	8 retrocopies	retro_cfam_1142, retro_cfam_1183, retro_cfam_1225, retro_cfam_133, retro_cfam_1397, retro_cfam_1736, retro_cfam_1889, retro_cfam_560,
Callithrix jacchus	ENSCJAG00000019987	4 retrocopies	retro_cjac_1716, retro_cjac_2022, retro_cjac_2813, retro_cjac_2911,
Cavia porcellus	ENSCPOG00000009502	1 retrocopy	retro_cpor_1353,
Felis catus	ENSFCAG00000004243	1 retrocopy	retro_fcat_519,
Homo sapiens	ENSG00000182944	1 retrocopy	retro_hsap_463,
Gorilla gorilla	ENSGGOG00000012212	1 retrocopy	retro_ggor_444,
Macropus eugenii	ENSMEUG00000008703	1 retrocopy	retro_meug_1424,
Myotis lucifugus	ENSMLUG00000012058	1 retrocopy	retro_mluc_328,
Monodelphis domestica	ENSMODG00000008679	1 retrocopy	retro_mdom_279 ,
Mustela putorius furo	ENSMPUG00000013432	2 retrocopies	retro_mputfur_56, retro_mputfur_572,
Mus musculus	ENSMUSG00000009079	1 retrocopy	retro_mmus_1379,
Oryctolagus cuniculus	ENSOCUG00000004432	2 retrocopies	retro_ocun_1346, retro_ocun_242,
Pongo abelii	ENSPPYG00000011684	1 retrocopy	retro_pabe_1769,
Pan troglodytes	ENSPTRG00000014218	1 retrocopy	retro_ptro_350,
Ictidomys tridecemlineatus	ENSSTOG00000023177	1 retrocopy	retro_itri_1892,
Tursiops truncatus	ENSTTRG00000011881	1 retrocopy	retro_ttru_1366,