RetrogeneDB ID: retro_mdom_1496

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 5:21684694..21685696(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMODG00000019192
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSMODG00000011916
• Aliases: None
• Description: None

Sequence

>retro_mdom_1496
CTCTTCCACCACCATTTTAATTCTGGCTCCATACTATGTACTGCCACTGCAACTCCCTCTCTGTGCCACCCGCCCGGGCT
GATAGCCCTGCGGCTAAGGAGGACGTGAATGAGTACAGCAATATGGAGGAGTTCGGGGAAGGATCCAAAATCAACGCCAG
CAAGAATCAGCAGGACCATGGTAAAATGTTTATTGGAGGGCTAAGCTGGGATATGAGCAAGAAAGATCTCACTGAATACC
TGTCTCGTTTTGGAGAGGTTTTGGAGACTGCACAATTAAAACAGATCCCATTATGGGAAGATCGAGGGGATACGGATTTG
TGCTTTTCAAAGATGCTGCCAGTGTCGATAAGGTTCTGGAACTTAAAGAACACAAGTTAGATGGCAAGTTGATAGACCCC
AAAAGGGCTAAATCTTTAAAGGGAAAGGAGCCCCCCCAAAAAAGTATTTGTCAGCGGACTGAGCCCAGATACCCCCAAAG
AACAAATCCAAGAATATTTTGGAGCATTTGGAGAGATTGAGAATATTGAACTTCCTATGGACACAAAAACAAATGAAAGA
AGAAAGATTCTGTTTTATCACATATACAGATGAAGAACCAGTAAAGAAATTATTAGAAAACAGATATCATCAGATTGGTT
CTGGGAAGTGTGAAATTAAAGTTGCCCAGACCAAAGAGGTATACAGGCAGCAACAGCAACAACAGAAATGAGGGAGGGGC
GCTGGAGCTGGTGGATGAGGTGGGACTAGGGGTTGTGGCTGAGGTCAGGGCCAAAACTGGAATCATGGATTTAATAACTA
TTATGATCAAGGATGTGGAAATTACAATAGTGCCTATGGTGGTGATCAAAACTATAGTGGCTATGGCGGATATAATTATA
CTGGGTATAACTATGGGAACTATGGATATGGACAGAGATATGCAGACTATAGTGGTCAACAAAGCACATGTGGCAAAGCA
TCCAGAGGGGGTGGTAATCACCAAAACAATTAACAACCATAT

Alignment

ORF - retro_mdom_1496 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.8 %
• Parental protein coverage: 79.86 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  LFRRHFKSGSIHRAAAATPSPRHLPP-ADSPAAMEDVNEYSNMEEFAEGSKINASKNQQDDGKMFIGGLS
          LF..HF.SGSI...A.ATPS..H.P..ADSPAA.EDVNEYSNMEEF.EGSKINASKNQQD.GKMFIGGLS
Retrocopy LFHHHFNSGSILCTATATPSLCHPPG<ADSPAAKEDVNEYSNMEEFGEGSKINASKNQQDHGKMFIGGLS

Parental  WDTSKKDLTEYLSRFGEVVD-CTIKTDP-VTGRSRGFGFVLFKDAASVDKVLELKEHKLDGKLIDPKRAK
          WD.SKKDLTEYLSRFGEV......K..P...GRSRG.GFVLFKDAASVDKVLELKEHKLDGKLIDPKRAK
Retrocopy WDMSKKDLTEYLSRFGEVLETAQLKQIP<IMGRSRGYGFVLFKDAASVDKVLELKEHKLDGKLIDPKRAK

Parental  ALKGKE-PPKKVFVGGLSPDTSEEQIKEYFGAFGEIENIELPMDTKTNERR-GFCFITYTDEEPVKKLLE
          .LKGKE.PPKKVFV.GLSPDT..EQI.EYFGAFGEIENIELPMDTKTNERR..FCFITYTDEEPVKKLLE
Retrocopy SLKGKE>PPKKVFVSGLSPDTPKEQIQEYFGAFGEIENIELPMDTKTNERR>RFCFITYTDEEPVKKLLE

Parental  NRYHQIGSGKCEIKVAQPKEVYRQQQQQQKGGRGAAAGGRGGTRGRGRGQGQNWNQGFNNYYDQGYGNYN
          NRYHQIGSGKCEIKVAQ.KEVYRQQQQQQK.GRGA.AGG.GGTRG.G.GQGQNWN.GFNNYYDQG.GNYN
Retrocopy NRYHQIGSGKCEIKVAQTKEVYRQQQQQQK*GRGAGAGG*GGTRGCG*GQGQNWNHGFNNYYDQGCGNYN

Parental  SAYGGDQNYSGYGGYDYTGYNYGNYGYGQGYADYSGQQSTYGKASRGGGNHQNNYQPY
          SAYGGDQNYSGYGGY.YTGYNYGNYGYGQ.YADYSGQQST.GKASRGGGNHQNN.QPY
Retrocopy SAYGGDQNYSGYGGYNYTGYNYGNYGYGQRYADYSGQQSTCGKASRGGGNHQNN*QPY

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_1496 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_1496 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 40 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000015197	1 retrocopy	retro_cjac_2589,
Dasypus novemcinctus	ENSDNOG00000003887	7 retrocopies	retro_dnov_1175, retro_dnov_1182, retro_dnov_144, retro_dnov_1603, retro_dnov_31, retro_dnov_723, retro_dnov_930,
Felis catus	ENSFCAG00000000455	1 retrocopy	retro_fcat_1568,
Macropus eugenii	ENSMEUG00000011454	7 retrocopies	retro_meug_1252, retro_meug_1378, retro_meug_1491, retro_meug_1971, retro_meug_2165, retro_meug_249, retro_meug_766,
Monodelphis domestica	ENSMODG00000011916	6 retrocopies	retro_mdom_1496 , retro_mdom_1789, retro_mdom_1951, retro_mdom_2017, retro_mdom_546, retro_mdom_981,
Monodelphis domestica	ENSMODG00000019803	1 retrocopy	retro_mdom_1590,
Otolemur garnettii	ENSOGAG00000002501	4 retrocopies	retro_ogar_2717, retro_ogar_2791, retro_ogar_437, retro_ogar_693,
Sarcophilus harrisii	ENSSHAG00000013616	3 retrocopies	retro_shar_297, retro_shar_527, retro_shar_625,
Ictidomys tridecemlineatus	ENSSTOG00000013979	1 retrocopy	retro_itri_1177,
Tupaia belangeri	ENSTBEG00000002817	7 retrocopies	retro_tbel_2079, retro_tbel_2283, retro_tbel_2608, retro_tbel_2874, retro_tbel_3344, retro_tbel_4302, retro_tbel_4405,
Tursiops truncatus	ENSTTRG00000001793	2 retrocopies	retro_ttru_1486, retro_ttru_744,