RetrogeneDB ID: retro_mdom_192

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 5:144011303..144012227(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMODG00000000016
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSMODG00000019001
• Aliases: None
• Description: None

Sequence

>retro_mdom_192
ATGGCGGAGGAGAAGTTCATTAAAGAGCTGAATCAATGGATGAAACGACTGAAAGATTGTCACATCTTCACAGAGAAGCA
AGTGCATACCCTATGTGAGAAGGCTAAGGAAATCCTAATGAAAGAATCAAACGTTAAGGAAGTCTCTAGTCCTGTTACAG
TCTGTGGCGATGTCCATGGCCAATTCCAGGACGTTTTGGAAATCTTTAGGATTGGTGGGAAATTACCAGACAAAAAGTAC
CTGTTTATGGGTGACTATGTTGACAGAGGCTTTTCCTCAGTGGAAACTATGACTTTTCTGCTATCCTTAAAAGTACAATA
TCCAGAGTTTATCACGCTATTGAGAGGAAACCACGAGTGTCGGGAGATTACTCAAGTGTATGGTTTTTATGATGAATGCC
AAAAGAAGTATGGAAATGCCAATGTCTGGAAATATTTTACAGACCTATTCGATTATCTTCCTATTACGGCTTTAGTTGAC
AAGCAGGTATTTTGCCTCCACGGGGGTCTGTCTCCCTCCATAGATACCTTGGATCATATAAGAGGTTTGAATCGATTTAA
AGAAATCCCCCAAACTGGACCAATGTGTGATCTGTTATGGTCTGATCCAGCTGATATTAAGGAATGGGAACCCTCCCCAA
GAGGGGCCGGCTACATATTTGGAGCGGACGTTTCTGAAATCTTTTCCCAGGCCAATGGTCTTGCACTGATTTCCCGGGGT
CACCAACTTGTCGAGTCCGGATTCAGCTTTTCTCATAACGGAAGGGTGCTGACCATTTTCAGTGCACCCAATTATTGTTA
CCGTTTTGGGAACCAAGCTGCTATCATGGAACTGGAAAGTCCTACAAAGTACTCCTTCATACAGTTTGAACAAGTACCTC
ATGTGAAGTGTTCTGTTTTCTCACTCCTACCTGATTCCTATAGA

Alignment

ORF - retro_mdom_192 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 71.33 %
• Parental protein coverage: 94.82 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MEDKIFTKELDQWVEQLNECKQLNENQVRTLCEKAKEILTKESNVQEVRCPVTVCGDVHGQFHDLMELFR
          M....F.KEL.QW...L..C....E.QV.TLCEKAKEIL.KESNV.EV..PVTVCGDVHGQF.D..E.FR
Retrocopy MAEEKFIKELNQWMKRLKDCHIFTEKQVHTLCEKAKEILMKESNVKEVSSPVTVCGDVHGQFQDVLEIFR

Parental  IGGKSPDTNYLFMGDYVDRGYYSVETVTLLVSLKVRYPERITILRGNHESRQITQVYGFYDECLRKYGNA
          IGGK.PD..YLFMGDYVDRG..SVET.T.L.SLKV.YPE.IT.LRGNHE.R.ITQVYGFYDEC..KYGNA
Retrocopy IGGKLPDKKYLFMGDYVDRGFSSVETMTFLLSLKVQYPEFITLLRGNHECREITQVYGFYDECQKKYGNA

Parental  NVWKYFTDLFDYLPLTALVDGQIFCLHGGLSPSIDTLDHIRALDRLQEVPHEGPMCDLLWSDPDDRGGWG
          NVWKYFTDLFDYLP.TALVD.Q.FCLHGGLSPSIDTLDHIR.L.R..E.P..GPMCDLLWSDP.D...W.
Retrocopy NVWKYFTDLFDYLPITALVDKQVFCLHGGLSPSIDTLDHIRGLNRFKEIPQTGPMCDLLWSDPADIKEWE

Parental  ISPRGAGYTFGQDISETFNHANGLTLVSRAHQLVMEGYNWCHDRNVVTIFSAPNYCYRCGNQAAIMELDD
          .SPRGAGY.FG.D.SE.F..ANGL.L.SR.HQLV..G....H...V.TIFSAPNYCYR.GNQAAIMEL..
Retrocopy PSPRGAGYIFGADVSEIFSQANGLALISRGHQLVESGFSFSHNGRVLTIFSAPNYCYRFGNQAAIMELES

Parental  TLKYSFLQFDPAP
          ..KYSF.QF...P
Retrocopy PTKYSFIQFEQVP

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_192 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_192 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 15 parental genes, and 29 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000001615	1 retrocopy	retro_amel_663,
Bos taurus	ENSBTAG00000009245	3 retrocopies	retro_btau_1199, retro_btau_1750, retro_btau_704,
Choloepus hoffmanni	ENSCHOG00000003467	9 retrocopies	retro_chof_1247, retro_chof_1521, retro_chof_1556, retro_chof_2112, retro_chof_2267, retro_chof_2502, retro_chof_251, retro_chof_273, retro_chof_446,
Callithrix jacchus	ENSCJAG00000012460	1 retrocopy	retro_cjac_985,
Dasypus novemcinctus	ENSDNOG00000010906	1 retrocopy	retro_dnov_2211,
Echinops telfairi	ENSETEG00000018123	4 retrocopies	retro_etel_1607, retro_etel_1923, retro_etel_680, retro_etel_702,
Felis catus	ENSFCAG00000025139	1 retrocopy	retro_fcat_1884,
Homo sapiens	ENSG00000104695	1 retrocopy	retro_hsap_1631,
Gorilla gorilla	ENSGGOG00000013978	1 retrocopy	retro_ggor_380,
Macaca mulatta	ENSMMUG00000020819	1 retrocopy	retro_mmul_484,
Monodelphis domestica	ENSMODG00000019001	2 retrocopies	retro_mdom_192 , retro_mdom_632,
Oryctolagus cuniculus	ENSOCUG00000005230	1 retrocopy	retro_ocun_1697,
Otolemur garnettii	ENSOGAG00000002488	1 retrocopy	retro_ogar_3188,
Pongo abelii	ENSPPYG00000018491	1 retrocopy	retro_pabe_335,
Tursiops truncatus	ENSTTRG00000000102	1 retrocopy	retro_ttru_1576,