RetrogeneDB ID: retro_mdom_1867

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 8:149429681..149430662(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSMODG00000006222
• Aliases: None
• Description: None

Sequence

>retro_mdom_1867
ATCTATATTAAGAACTTGGATGACACCATTGATGATGAAAAATTAAAGAAGGTATTTTCTCCTTTTTGATCAATTACCAG
TTGCAAGGTGATGCTAGAAGATGGGAGAATTAAAGGCTTTGTCTTTGTCTGCTTCTCTTCACTTGATGAGGCAACCAAAG
CAGTAACAGAAATGAATGGGTGCATTGTGGGCTCAAAGCCCTCCTATGTTGCACTTGCACAGAGGAAAAAAGAAAGGAAA
GCTCACCTAACCAATCAGTATATGCAGCCTATCCCAGGAATGAGAGCCCTACCCACCAACACTATCATCAATCAGTTTCA
GCCAACTCCTGGGGGCTACTTCATGCCAGCAGTGCCCCAGGCTCAGAATAGACCTCCTTATTATGCTCCCAATCAGATAA
CCCAGATGAGACCCAATCCCTGATGGCAACAAGGTGGAAGACCTCAAGGCTTTCAAGGAGTACCAAGCACCATTCGTCAA
TCTGGACAGCACCCTGCTCTTCAACACCTGACTCCAGCCAGTAATACCCAGGCTTCTCGAGGGCTCCCTACTATATCTCA
GAGAGTGGGGGTGCCCACTGCTGTGCAGAATTTATCTCCTAGACTCTCTGTAGCTACCCCTGCACCTCAAGCCATCCCTC
CTTACAAATATGCTGCAAATGTCCGAAGCCCCCATCCAGCCCTCCAGCCTTTGCAGACACCTCAACCAGCAGTCCATGTG
CAAGGCCAGGAGCCCTTGACAGCTTCAATGCTGGCTGCTACTCCTCCCCAGGAACAGAAGCAGATGCTAGGAGAGCGCTT
GTTCCCATTGATTCAAACCATGCACAATAATTTATCAGGGAAGATCACAGGTATGCTGCTAGAAATAGATAATTCAGAAC
TGCTGCACATGCTGGAGTCTCCTGAATCCCTCTGTCCAAAGTTGGAGGAAGCCATACCAGTATTACAAGCTTGTCACACC
AAGAAGGAAGCTGCTCAGAAG

Alignment

ORF - retro_mdom_1867 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 63.88 %
• Parental protein coverage: 51.74 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  LYVKNLDDGIDDERLRKEFSPFGTITSAKVMMEGGRSKGFGFVCFSSPEEATKAVTEMNGRIVATKPLYV
          .Y.KNLDD.IDDE.L.K.FSPF..ITS.KVM.E.GR.KGF.FVCFSS..EATKAVTEMNG.IV..KP.YV
Retrocopy IYIKNLDDTIDDEKLKKVFSPF*SITSCKVMLEDGRIKGFVFVCFSSLDEATKAVTEMNGCIVGSKPSYV

Parental  ALAQRKEERQAHLTNQYMQRMASVRAVP-NPVINPYQP-PSGYFMAAIPQTQNRAAYYPASQIAQLRPSP
          ALAQRK.ER.AHLTNQYMQ.....RA.P.N..IN..QP.P.GYFM.A.PQ.QNR..YY...QI.Q.RP.P
Retrocopy ALAQRKKERKAHLTNQYMQPIPGMRALPTNTIINQFQPTPGGYFMPAVPQAQNRPPYYAPNQITQMRPNP

Parental  RWTAQGARPHPFQNMPGAIRPAAPRPPFSTMRPAS-SQVPRVMST--QRV-ANTSTQTMGPRPAAAAAAA
          .W..QG.RP..FQ..P..IR.....P......PAS..Q..R...T..QRV...T..Q...PR...A....
Retrocopy *W-QQGGRPQGFQGVPSTIRQSGQHPALQHLTPASNTQASRGLPTISQRVGVPTAVQNLSPRLSVA----

Parental  TPAVRTVPQYKYAAGVRNPQQHLNAQPQVTMQQPAVHVQGQEPLTASMLASAPPQEQKQMLGERLFPLIQ
          TPA....P.YKYAA.VR.P..H...QP..T..QPAVHVQGQEPLTASMLA..PPQEQKQMLGERLFPLIQ
Retrocopy TPAPQAIPPYKYAANVRSP--HPALQPLQT-PQPAVHVQGQEPLTASMLAATPPQEQKQMLGERLFPLIQ

Parental  AMHPTLAGKITGMLLEIDNSELLHMLESPESLRSKVDEAVAVLQA-HQAKEAAQK
          .MH..L.GKITGMLLEIDNSELLHMLESPESL..K..EA..VLQA.H..KEAAQK
Retrocopy TMHNNLSGKITGMLLEIDNSELLHMLESPESLCPKLEEAIPVLQACHTKKEAAQK

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_1867 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_1867 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 24 parental genes, and 49 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000000348	1 retrocopy	retro_amel_1650,
Choloepus hoffmanni	ENSCHOG00000008178	1 retrocopy	retro_chof_2531,
Callithrix jacchus	ENSCJAG00000015833	5 retrocopies	retro_cjac_1586, retro_cjac_2571, retro_cjac_3218, retro_cjac_4039, retro_cjac_41,
Cavia porcellus	ENSCPOG00000012917	1 retrocopy	retro_cpor_1324,
Dasypus novemcinctus	ENSDNOG00000008718	2 retrocopies	retro_dnov_1530, retro_dnov_2259,
Felis catus	ENSFCAG00000001874	1 retrocopy	retro_fcat_1927,
Homo sapiens	ENSG00000070756	1 retrocopy	retro_hsap_88,
Gorilla gorilla	ENSGGOG00000006785	1 retrocopy	retro_ggor_1986,
Myotis lucifugus	ENSMLUG00000012245	1 retrocopy	retro_mluc_579,
Macaca mulatta	ENSMMUG00000017786	2 retrocopies	retro_mmul_1462, retro_mmul_895,
Monodelphis domestica	ENSMODG00000006222	4 retrocopies	retro_mdom_123, retro_mdom_1867 , retro_mdom_216, retro_mdom_43,
Monodelphis domestica	ENSMODG00000017657	2 retrocopies	retro_mdom_1090, retro_mdom_1805,
Mus musculus	ENSMUSG00000022283	2 retrocopies	retro_mmus_102, retro_mmus_2164,
Nomascus leucogenys	ENSNLEG00000003142	3 retrocopies	retro_nleu_221, retro_nleu_2412, retro_nleu_611,
Oryctolagus cuniculus	ENSOCUG00000004354	1 retrocopy	retro_ocun_13,
Pongo abelii	ENSPPYG00000018790	3 retrocopies	retro_pabe_2373, retro_pabe_68, retro_pabe_854,
Pteropus vampyrus	ENSPVAG00000016640	2 retrocopies	retro_pvam_10, retro_pvam_855,
Rattus norvegicus	ENSRNOG00000008639	3 retrocopies	retro_rnor_1228, retro_rnor_2321, retro_rnor_265,
Sarcophilus harrisii	ENSSHAG00000011267	1 retrocopy	retro_shar_24,
Sus scrofa	ENSSSCG00000006063	2 retrocopies	retro_sscr_1153, retro_sscr_1205,
Ictidomys tridecemlineatus	ENSSTOG00000016395	2 retrocopies	retro_itri_139, retro_itri_48,
Tarsius syrichta	ENSTSYG00000004229	2 retrocopies	retro_tsyr_1743, retro_tsyr_273,
Tursiops truncatus	ENSTTRG00000004689	2 retrocopies	retro_ttru_1050, retro_ttru_1812,
Vicugna pacos	ENSVPAG00000003865	4 retrocopies	retro_vpac_14, retro_vpac_384, retro_vpac_620, retro_vpac_649,