RetrogeneDB ID: retro_mdom_229

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 6:88924168..88925074(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMODG00000024888
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSMODG00000013383
• Aliases: None
• Description: None

Sequence

>retro_mdom_229
ATGGTGTCCCAGGAGAGGAAAACAGAGGGAACCCTTAACTCCTTGAAGAACTTCCTGGCGGGAGGTTTCGGGGGCATGTG
CGTGGTGTTCGTGGGCCACCCGCTGGACACGGTGAAGGTAAGGCTACAGACCCAGCCGAAGAGCCGGCTAGGACAACCTA
CCCTCTACTCTGGGACCTTTGACTGTTTCCGAAAGACCTTTCTTAGGGAGGGTATTGGAGGCCTTTACCGAGGAATGAGC
GCACCGCTCATTGGTGTCACGCCCATATTCGCCGTTTGCTTCTTTGGCTTTGGACTGGGGAAACAACTGCAACAGAAGAA
CCCGGATGACGTCTTGACTTACCCCCAGCTGTTTGTAGCTGGGATGTTATCTGGCGTGTTCACTACGGCCATCATGACTC
CTATAGAAAGAATCAAGTGCCTATTACAGATTCAAGCTTCTCAAGGAAAAACAAAATATACTGGTTCTTGGGACTGTCTC
AAAGCTGTCTATCGGGAAGCTGGAATAAGAGGCATTTTCAAAGGAACTGTGCTCACGCTCATGCGAGATGTACCTGCCAG
TGGGGTGTACTTCATGACTTACGAATGGCTGAAAAATGTCTTCACCGTAGAAAGAAAAATTGGTGCTGCTGGAATTGTGG
TGGCTGGAGGCATGGCAGGCATCTTCAACTGGATGGTGGCTATCCCTCCTGATGTGCTCAAGTCTCGCTTCCAGACTGCC
CCACCTGGAAAATACCCTAATGGGTTCCGAGATGTACTGAAAGAGGTGGTCCAAGAAGGGGGTGTATCATCCTTGTATAA
AGGTTTTACAGCCGTAATGATCCGTGCCTTCCCAGCAAATGCTGCCTGTTTCCTTGGTTTTGAGGTTGCCTTGGCAGTCC
TTAATTGGATCACATCTAAGTTCTGA

Alignment

ORF - retro_mdom_229 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 78.45 %
• Parental protein coverage: 98.67 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  ELEEKAPISPLKNFLAGGFGGMCLVFVGHPLDTVKVRLQTQPKGQQGQPSLYSGTFDCFRKTLVKEGIQG
          E.........LKNFLAGGFGGMC.VFVGHPLDTVKVRLQTQPK...GQP.LYSGTFDCFRKT...EGI.G
Retrocopy ERKTEGTLNSLKNFLAGGFGGMCVVFVGHPLDTVKVRLQTQPKSRLGQPTLYSGTFDCFRKTFLREGIGG

Parental  LYRGMAAPIIGVTPMFAVCFFGFGLGKKLQQKNPDDVLTYPQLFAAGMLSGVFTTGIMTPGERIKCLLQI
          LYRGM.AP.IGVTP.FAVCFFGFGLGK.LQQKNPDDVLTYPQLF.AGMLSGVFTT.IMTP.ERIKCLLQI
Retrocopy LYRGMSAPLIGVTPIFAVCFFGFGLGKQLQQKNPDDVLTYPQLFVAGMLSGVFTTAIMTPIERIKCLLQI

Parental  QASSGETKYTGALDCAKKVYQESGIRGIYKGTMLTLLRDVPASGMYFMTYEWLKNILTPEGKSVNELSVP
          QAS.G.TKYTG..DC.K.VY.E.GIRGI.KGT.LTL.RDVPASG.YFMTYEWLKN..T.E.K........
Retrocopy QASQGKTKYTGSWDCLKAVYREAGIRGIFKGTVLTLMRDVPASGVYFMTYEWLKNVFTVERK----IGAA

Parental  QILFAGGAAGIFNWVVAIPPDVLKSRFQTAPPGKYPNGFQDVLRELIREEGITSLYKGFTAVMIRAFPAN
          .I..AGG.AGIFNW.VAIPPDVLKSRFQTAPPGKYPNGF.DVL.E...E.G..SLYKGFTAVMIRAFPAN
Retrocopy GIVVAGGMAGIFNWMVAIPPDVLKSRFQTAPPGKYPNGFRDVLKEVVQEGGVSSLYKGFTAVMIRAFPAN

Parental  AACFLGFEVALKFLNWI
          AACFLGFEVAL..LNWI
Retrocopy AACFLGFEVALAVLNWI

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_229 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_229 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 9 parental genes, and 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000003285	1 retrocopy	retro_cjac_2338,
Homo sapiens	ENSG00000178537	1 retrocopy	retro_hsap_3469,
Gorilla gorilla	ENSGGOG00000028046	1 retrocopy	retro_ggor_2341,
Macaca mulatta	ENSMMUG00000015418	1 retrocopy	retro_mmul_1764,
Monodelphis domestica	ENSMODG00000013383	3 retrocopies	retro_mdom_1584, retro_mdom_229 , retro_mdom_266,
Nomascus leucogenys	ENSNLEG00000006700	1 retrocopy	retro_nleu_342,
Pongo abelii	ENSPPYG00000013892	1 retrocopy	retro_pabe_2865,
Pan troglodytes	ENSPTRG00000014900	1 retrocopy	retro_ptro_2352,
Drosophila melanogaster	FBgn0031881	1 retrocopy	retro_dmel_15,