RetrogeneDB ID: retro_mdom_1337

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 4:58955162..58955898(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMODG00000001857
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSMODG00000010398
• Aliases: None
• Description: None

Sequence

>retro_mdom_1337
GGGAACACCACCAAAAAATGCTATGAGAAGCTGTTTGAGTATTATAAGAATGGAGACCTGTCCTTCAAGTATGTGAAAAC
ATTTAAAATGGATGAGTATGTGGGCCTCCCACTTGACTCCTCTCATAGCTTTCACACCTTCATGTGGGAGAAATTCTTCA
AGTATATTGATATTATCCCTGAAAACACCCATGTCCTGTATGGGAATACAGCTGATCTGCAGGAAGAATGTGAAGCTTTT
GAAGAGAAGTTCAAGGAAGCTGGAGGGATCAAGCTCTTTGTTGGAGGTATTGGTCCTGATGGGCATGTGCCTTCAATGAG
CCTGGCTCAAGTTTGGTGTGCAGGACCCAAGTGAAAACTCTGGTCATGGATACCATTCTAGCCAATGCCTGGTCCTTCAA
TGGAAAAAACTTCCAAGTCCCCATGATGGCTCTGACTGTGGGTGCAGGCACAGTCATAGATGCAGGAGAGGTCATGATCT
TAATTACAGGGCCCATAAGGCATCTGCATTGTGTAAGGCCATTGAGGAAGAGATAAATTACATCTGGACTGTTTCTGTTT
TCGAACAGCACCCCCAAACAATATTCACTTGTGATGAAGGTGCCACACTGGACCTTAAAGGGAAAACTGTAAAATATTTC
AAAAGGTTGATGTTTGATCATAACAAGATAGTGGAACCACTGTACAGTATAAAAGAAATAGCAACAGAAACAGAGACAAA
CCATTCTACCAAGAAA

Alignment

ORF - retro_mdom_1337 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 79.03 %
• Parental protein coverage: 98.4 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  GSTPEKCYQKLIEYYKNGDLSFKYVKTFNMDEYVGLPRDHSQSYHTFMWEKLFKHIDISPENTHILDGNA
          G.T..KCY.KL.EYYKNGDLSFKYVKTF.MDEYVGLP.D.S.S.HTFMWEK.FK.IDI.PENTH.L.GN.
Retrocopy GNTTKKCYEKLFEYYKNGDLSFKYVKTFKMDEYVGLPLDSSHSFHTFMWEKFFKYIDIIPENTHVLYGNT

Parental  ADLQAECDAFEEKIKEAGGIELFVGGIGPDGHV-AFNEPGSSLVSRTRVKTLAMDTILANARFFDGKNSQ
          ADLQ.EC.AFEEK.KEAGGI.LFVGGIGPDGHV.AFNEPGSSLV.RT.VKTL.MDTILANA..F.GKN.Q
Retrocopy ADLQEECEAFEEKFKEAGGIKLFVGGIGPDGHV<AFNEPGSSLVCRTQVKTLVMDTILANAWSFNGKNFQ

Parental  VPTMALTVGVGTVMDAREVMILITG-AHKAFALHKAIEEGINHMWTVSAFQQHPQTIFVCDEDATLELKV
          VP.MALTVG.GTV.DA.EVMILITG.AHKA.AL.KAIEE.IN..WTVS.F.QHPQTIF.CDE.ATL.LK.
Retrocopy VPMMALTVGAGTVIDAGEVMILITG<AHKASALCKAIEEEINYIWTVSVFEQHPQTIFTCDEGATLDLKG

Parental  KTVKYFKGLMLVHNKLVEPLYSIKETETKTETSHSTKK
          KTVKYFK.LM..HNK.VEPLYSIKE..T.TET.HSTKK
Retrocopy KTVKYFKRLMFDHNKIVEPLYSIKEIATETETNHSTKK

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	16.09 RPM
SRP007412_cerebellum	0.00 RPM	15.34 RPM
SRP007412_heart	0.00 RPM	17.14 RPM
SRP007412_kidney	0.00 RPM	76.38 RPM
SRP007412_liver	0.00 RPM	24.17 RPM
SRP007412_testis	0.00 RPM	30.25 RPM

ChIP-Seq

Monodelphis domestica was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mdom_1337 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_1337 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 17 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000007865	1 retrocopy	retro_btau_535,
Choloepus hoffmanni	ENSCHOG00000009884	2 retrocopies	retro_chof_2278, retro_chof_42,
Dasypus novemcinctus	ENSDNOG00000007804	3 retrocopies	retro_dnov_1363, retro_dnov_1608, retro_dnov_508,
Macropus eugenii	ENSMEUG00000015442	1 retrocopy	retro_meug_655,
Monodelphis domestica	ENSMODG00000010398	1 retrocopy	retro_mdom_1337 ,
Monodelphis domestica	ENSMODG00000020593	1 retrocopy	retro_mdom_67,
Mus musculus	ENSMUSG00000052102	1 retrocopy	retro_mmus_2711,
Oryctolagus cuniculus	ENSOCUG00000016963	1 retrocopy	retro_ocun_1266,
Otolemur garnettii	ENSOGAG00000007303	3 retrocopies	retro_ogar_2251, retro_ogar_2506, retro_ogar_446,
Ictidomys tridecemlineatus	ENSSTOG00000016508	1 retrocopy	retro_itri_1135,
Tupaia belangeri	ENSTBEG00000003330	2 retrocopies	retro_tbel_2431, retro_tbel_59,