RetrogeneDB ID: retro_mdom_256

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 4:295453388..295454069(+)
• Located in intron of: ENSMODG00000008674

Retrocopy information

• Ensembl ID: ENSMODG00000008684
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSMODG00000016129
• Aliases: None
• Description: None

Sequence

>retro_mdom_256
TTGGGGCCGGAGGCTGCAGGCGGTGATGAGGCGCCGTGCGCGCTGCTTCTCCTGCTTTGGCTGGCCTTCGCTTCAGTGCA
GGGTCTTTATTTCCACATCGGAGAGACGGAGAAGTGCTGCTTCATTGAGGAAAGCCCCAACGAGACCATAGTTATCGGGA
TTTACCGAACCCAGCTATGGGATAAGCAGACCGAGACCTTTCTGCCCTCCACCCCGGGGCTGGGGATGCATGTGGAAGTG
AAGAATCCTGAAGGAAAGGTGGTATTATCGTGGCAGTATGGTTCAGAGGGCCGATTCACCTTTACTTCCCATACCCCAGG
TGACCACCAGATCTGCCTGCACTCTAATTCTACTAGAATGACCATCTTTGCGGGCGGCAAACTTAGAGTACATCTGGATA
TACAGGTTGGCGAACATACCAACAACTACCCTGAAATTGCTGCCAAGGATAAATTAACAGAGCTACAACTTCCTGCCGGC
CAGTTGCTTGATCAGGTGGAACAGATCCAAGAGGAACAGAACTACCAGCCGTATCGTGAAGAACGCTTCCGTATGACCAG
CGAGAGCACAAACCAGAGAGTGCTGTGGTGGTCCATTGCTCAGACTATCATCCTTATCCTCACTGGCAAATGGCAGATGA
GACACCTCAAGAGTTTCTTTGAGGCCAAAAAGCTGGTGTAA

Alignment

ORF - retro_mdom_256 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 93.9 %
• Parental protein coverage: 91.81 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  ALLLLLWLAFASVQGLYFHIGETEKRCFIEEIPDETMVIGNYRTQLWDKQTETFLPSTPGLGMHVEVKDP
          ALLLLLWLAFASVQGLYFHIGETEK.CFIEE.P.ET.VIG.YRTQLWDKQTETFLPSTPGLGMHVEVK.P
Retrocopy ALLLLLWLAFASVQGLYFHIGETEKCCFIEESPNETIVIGIYRTQLWDKQTETFLPSTPGLGMHVEVKNP

Parental  EGKVVLSRQYGSEGRFTFTSHTPGDHQICLHSNSTRMTIFAGGKLRVHLDIQVGEHTNNYPEIAAKDKLT
          EGKVVLS.QYGSEGRFTFTSHTPGDHQICLHSNSTRMTIFAGGKLRVHLDIQVGEHTNNYPEIAAKDKLT
Retrocopy EGKVVLSWQYGSEGRFTFTSHTPGDHQICLHSNSTRMTIFAGGKLRVHLDIQVGEHTNNYPEIAAKDKLT

Parental  ELQLRARQLLDQVEQIQKEQNYQRYREERFRMTSESTNQRVLWWSIAQTVILILTGIWQMRHLKSFFEAK
          ELQL.A.QLLDQVEQIQ.EQNYQ.YREERFRMTSESTNQRVLWWSIAQT.ILILTG.WQMRHLKSFFEAK
Retrocopy ELQLPAGQLLDQVEQIQEEQNYQPYREERFRMTSESTNQRVLWWSIAQTIILILTGKWQMRHLKSFFEAK

Parental  KLV
          KLV
Retrocopy KLV

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	245.43 RPM
SRP007412_cerebellum	0.00 RPM	363.34 RPM
SRP007412_heart	0.00 RPM	495.39 RPM
SRP007412_kidney	0.00 RPM	659.73 RPM
SRP007412_liver	0.00 RPM	502.48 RPM
SRP007412_testis	0.00 RPM	274.61 RPM

ChIP-Seq

Monodelphis domestica was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mdom_256 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_256 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 5 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Erinaceus europaeus	ENSEEUG00000007627	2 retrocopies	retro_eeur_12, retro_eeur_317,
Macropus eugenii	ENSMEUG00000006810	1 retrocopy	retro_meug_1225,
Monodelphis domestica	ENSMODG00000016129	2 retrocopies	retro_mdom_256 , retro_mdom_362,
Oryctolagus cuniculus	ENSOCUG00000003964	1 retrocopy	retro_ocun_1909,
Ictidomys tridecemlineatus	ENSSTOG00000014658	1 retrocopy	retro_itri_1499,