RetrogeneDB ID: retro_mdom_159

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 1:387190807..387191452(-)
• Located in intron of: ENSMODG00000002830

Retrocopy information

• Ensembl ID: ENSMODG00000002836
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSMODG00000015178
• Aliases: None
• Description: None

Sequence

>retro_mdom_159
ATGCAGCAGCCACCACGGCAGCCCGAGTTAGGGGAAGGCAATCTTCCTGTGTTCGTGTTCCCTACGGAGCTGATCTTTTA
TGCGGACGACCAGTCCACCCACAAGCAGGTGCTGACTCTCTATAATCCTTACGAGTTTGCCTTAAAGTTCAAAGTGCTGT
GCACCACCCCCATCAAGTACGTGGTGGTGGACGCCGCGGGGGCAGTGAAACCTCAGTGCTGCGTGGACATCGTCATTCGT
CACAGAGATGTCCGGCCCTGTCACTATGATGTAATAGACAAATTCCGGCTTCAAGTTTCGGAACAAAGCCAGGGGAAGCC
TTTAGGGCGCAAAGAGATTATTGCGACCCTTCTGCCGTCGGCTAAAGAACAGCGAAAGGAAGAAGAGGAAAAAAGGTTAA
AGGAACACTTGGCAGAAAGTGTCTTTTTTGAGCAGATGCTGTGTCAAACGGAAAACAGGACTGGCTCATCGGGACCTAGT
TTATTAACTGTCTTCCTGGGAATAGTGTGCATTGCAGCTCTGATGCTTCCCACACTGGGAGAAGTAGAATCTCTAGTGCC
TCACTACTTCCATTTAAGTGTGAATCAAAAATTAGTGGCTGCTTATGTTTTAGGTCTTATCACTATGGTTATACTTAGAA
TATGA

Alignment

ORF - retro_mdom_159 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 91.16 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MQQQRSQPELVEGNLPVFVFPTELIFYADDQSTHKQVLTLYNPYEFALKFKVLCTTPNKYVVVDAAGAVK
          MQQ...QPEL.EGNLPVFVFPTELIFYADDQSTHKQVLTLYNPYEFALKFKVLCTTP.KYVVVDAAGAVK
Retrocopy MQQPPRQPELGEGNLPVFVFPTELIFYADDQSTHKQVLTLYNPYEFALKFKVLCTTPIKYVVVDAAGAVK

Parental  PLCCVDIVIRHRDVRSCHYDVIDKFRLQVSEQSQRKALGRKEIIATLLPSAKEQRKEVEEKRIKEHLTES
          P.CCVDIVIRHRDVR.CHYDVIDKFRLQVSEQSQ.K.LGRKEIIATLLPSAKEQRKE.EEKR.KEHL.ES
Retrocopy PQCCVDIVIRHRDVRPCHYDVIDKFRLQVSEQSQGKPLGRKEIIATLLPSAKEQRKEEEEKRLKEHLAES

Parental  VFLKEHMLYQTENRNVSSGPSLLTVFLGIVCIAALMLPTLGEVESLVPLYFHLSVNQKLVAAYVLGLITM
          VF..E.ML.QTENR..SSGPSLLTVFLGIVCIAALMLPTLGEVESLVP.YFHLSVNQKLVAAYVLGLITM
Retrocopy VFF-EQMLCQTENRTGSSGPSLLTVFLGIVCIAALMLPTLGEVESLVPHYFHLSVNQKLVAAYVLGLITM

Parental  VILRI
          VILRI
Retrocopy VILRI

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	15.73 RPM	0.00 RPM
SRP007412_cerebellum	26.44 RPM	0.00 RPM
SRP007412_heart	7.77 RPM	0.00 RPM
SRP007412_kidney	7.90 RPM	0.00 RPM
SRP007412_liver	13.59 RPM	0.00 RPM
SRP007412_testis	16.11 RPM	0.00 RPM

ChIP-Seq

Monodelphis domestica was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mdom_159 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_159 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 11 parental genes, and 19 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000001304	1 retrocopy	retro_amel_683,
Choloepus hoffmanni	ENSCHOG00000007386	5 retrocopies	retro_chof_1202, retro_chof_1623, retro_chof_201, retro_chof_2295, retro_chof_675,
Dasypus novemcinctus	ENSDNOG00000013117	4 retrocopies	retro_dnov_1825, retro_dnov_2650, retro_dnov_2660, retro_dnov_926,
Macaca mulatta	ENSMMUG00000022505	1 retrocopy	retro_mmul_133,
Monodelphis domestica	ENSMODG00000015178	1 retrocopy	retro_mdom_159 ,
Mus musculus	ENSMUSG00000023074	1 retrocopy	retro_mmus_291,
Otolemur garnettii	ENSOGAG00000005739	2 retrocopies	retro_ogar_2508, retro_ogar_528,
Sarcophilus harrisii	ENSSHAG00000011544	1 retrocopy	retro_shar_21,
Sus scrofa	ENSSSCG00000012686	1 retrocopy	retro_sscr_690,
Ictidomys tridecemlineatus	ENSSTOG00000008152	1 retrocopy	retro_itri_1303,
Tarsius syrichta	ENSTSYG00000006102	1 retrocopy	retro_tsyr_1785,