RetrogeneDB ID: retro_mdom_1008

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 3:199952070..199952744(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: None
• Aliases: None
• Status: NOVEL

Parental gene information

• Parental gene symbol: GHITM
• Ensembl ID: ENSMODG00000001693
• Aliases: None
• Description: growth hormone inducible transmembrane protein [Source:HGNC Symbol;Acc:17281]

Sequence

>retro_mdom_1008
CTGAGGAATTTCATTCTGAAGACAAATAATCAATGGCTCTTATAATCCAACAGAGGCTATACCACCAAATCAAGAGTTGG
AGTCCAGCATGTAAAAACCAGTCAAGAAATTAAGCAAGCAGCTTTTGGACCATCAACAGAAAAAGTGTTTAAAATTGATC
ATATGGGAAGATAGTTTGTTGCTGGAGTAGCTGCTGTTGGCCTTGGAGCACTCAACTTCTATGGCTTGGAAATGTCAAGT
GAGATTGGGGCTATTGAAAAAGCAATAATCTGACCTCAGTATGTGGATAGAATTCATGCTACCTATAAGTATTTCACATG
GAGTGTTGGTTTAACAACATTATCTGCCTTAGCAATTAGTCGATCACCTGGTTTAATGGCCTTTATGATGAAAGGCTCTT
GGTTGGCAATCAGATCAACTTTTGCTGCTATACTGAGTGTTGGAATGATGGTTCAGTCAATATATGAACACAATTCAGGC
CTAAAACATCTTGCTTTAATGGCTCATTCTGGTGTCATGGGTGCAGTGGTGGCCCCCTAACTTTGCTGGGTGGCCCTTTG
ATCCTCTGAGCTGCTTGGTATACAGCAGGCACTGTGGGAGGCCTCTCTACTGTGGCCATGTGTGCTCCAAGTGAAAAATT
TCTAAACATGGGAGCACAACTGTCTTTGTTTCTT

Alignment

ORF - retro_mdom_1008 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 82.89 %
• Parental protein coverage: 63.06 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  LRNSILKTNNQWLLQSNKGYTTKSRIGVQRAKPDQEIKQAAFEPSAEKVFKIDQMGRWFVAGGAAVGLGA
          LRN.ILKTNNQWLL.SN.GYTTKSR.GVQ..K..QEIKQAAF.PS.EKVFKID.MGR.FVAG.AAVGLGA
Retrocopy LRNFILKTNNQWLL*SNRGYTTKSRVGVQHVKTSQEIKQAAFGPSTEKVFKIDHMGR*FVAGVAAVGLGA

Parental  LCFYGLGMSNEIGAIEKAVIWPQYVKDRIHATYMYFAGSVGLTALSALAISRSPGLMAFMMKGSWLAIGA
          L.FYGL.MS.EIGAIEKA.I.PQYV.DRIHATY.YF..SVGLT.LSALAISRSPGLMAFMMKGSWLAI..
Retrocopy LNFYGLEMSSEIGAIEKAII*PQYV-DRIHATYKYFTWSVGLTTLSALAISRSPGLMAFMMKGSWLAIRS

Parental  TFAAMVGAGMMVRSISYEHNSGLKHLAWMAHSGVMGAVVA-PLTLLGGPLILRAAWYTAGIVGGLSTVAM
          TFAA....GMMV.SI.YEHNSGLKHLA.MAHSGVMGAVVA.PLTLLGGPLIL.AAWYTAG.VGGLSTVAM
Retrocopy TFAAILSVGMMVQSI-YEHNSGLKHLALMAHSGVMGAVVA<PLTLLGGPLIL*AAWYTAGTVGGLSTVAM

Parental  CAPSEKFLNMGAPLGVGL
          CAPSEKFLNMGA.L...L
Retrocopy CAPSEKFLNMGAQLSLFL

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	386.56 RPM
SRP007412_cerebellum	0.00 RPM	389.13 RPM
SRP007412_heart	0.00 RPM	1672.56 RPM
SRP007412_kidney	0.00 RPM	816.44 RPM
SRP007412_liver	0.00 RPM	629.86 RPM
SRP007412_testis	0.00 RPM	2595.67 RPM

ChIP-Seq

Monodelphis domestica was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mdom_1008 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_1008 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 18 parental genes, and 28 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000009753	1 retrocopy	retro_amel_336,
Bos taurus	ENSBTAG00000032829	2 retrocopies	retro_btau_1689, retro_btau_779,
Choloepus hoffmanni	ENSCHOG00000001576	1 retrocopy	retro_chof_5,
Cavia porcellus	ENSCPOG00000006432	1 retrocopy	retro_cpor_1436,
Dasypus novemcinctus	ENSDNOG00000018880	5 retrocopies	retro_dnov_2426, retro_dnov_2514, retro_dnov_2524, retro_dnov_708, retro_dnov_812,
Dipodomys ordii	ENSDORG00000001109	1 retrocopy	retro_dord_184,
Echinops telfairi	ENSETEG00000001796	1 retrocopy	retro_etel_68,
Loxodonta africana	ENSLAFG00000009646	1 retrocopy	retro_lafr_388,
Macropus eugenii	ENSMEUG00000009861	3 retrocopies	retro_meug_1431, retro_meug_1806, retro_meug_798,
Microcebus murinus	ENSMICG00000011621	1 retrocopy	retro_mmur_692,
Monodelphis domestica	ENSMODG00000001693	3 retrocopies	retro_mdom_1008 , retro_mdom_407, retro_mdom_886,
Oryctolagus cuniculus	ENSOCUG00000006093	1 retrocopy	retro_ocun_260,
Otolemur garnettii	ENSOGAG00000012120	1 retrocopy	retro_ogar_1287,
Rattus norvegicus	ENSRNOG00000013961	1 retrocopy	retro_rnor_2461,
Sus scrofa	ENSSSCG00000010345	1 retrocopy	retro_sscr_1102,
Tupaia belangeri	ENSTBEG00000016365	2 retrocopies	retro_tbel_1601, retro_tbel_2819,
Tarsius syrichta	ENSTSYG00000006367	1 retrocopy	retro_tsyr_4,
Drosophila melanogaster	FBgn0030263	1 retrocopy	retro_dmel_61,