RetrogeneDB ID: retro_mdom_1119

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 3:155041400..155042449(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: DBR1
• Ensembl ID: ENSMODG00000018554
• Aliases: None
• Description: debranching RNA lariats 1 [Source:HGNC Symbol;Acc:15594]

Sequence

>retro_mdom_1119
AAATCCTTCTTTCAACAATAAGTAGAAAACAACACGTTGGGAAGCCCTGCTGCTTCAGATCTTTTACATCTTCTGCAACG
TACTTACTGGTTCTCTGCACACCTTCATGTGAAGTTTGCAGCTGTCATGAAACATCAGGCCAATGATGGGCAGGCACCAA
AAGAAACCAAAATTTTAGCCTTAGACAAATGTCTGCCCCACAGAGACTTCCTACAGATATTAGAAGTAGACCATGATGTA
AATGCACCAGACTATTTTGACTATGACCTGGAATGGCTCACTATTTTAAAGGCTACTAATAGTCTTGTAAATATGTCATG
AAGCTTATGGAATATGCCTGAAAATAATGACCTCCAAGCAAAGTGGGATTATAGTGCAACAGAAGAATCTAGGAAAGAGG
TATTGGAAGAAATGAACCAAGATCTCAAAGTTCCATATAACTTCAGTCTGACAGCTATATATGATCCCAGCAAGCCCCAG
AAACACATGGAATTAGTTCATAGGATCAGTCCTCAGACCACAGAATTGTGTGCCCAGGTTGGCCTCACTGATATGAATAA
TCAAATTCAACAAGTGATAGAAAAAAGTTCATTGTGTGGAGACTATGAGAAGGATGTGGACAATAATGGATCAGAAGAAC
CAAGAGTATACAACACAGATAATTCAGTCTTATCTTCTTCAATTAACCCAGATGAAATAATGCTTGATGAGGATGATGAG
GGTGAAGATGGTATTACAGTCATACATGGTGACTTTAGTATTCCCTCAGTGGAACCCTCATCTGATCATCACCTTCCTGA
TTTTTCAACAAGCTTTTCTGACATTAGGATCTTACCAGATTCCATGGTAGTATATTCTGATGATACCATGATTTCTACAA
ATGAACTGGAGAAATCTGGTAAAAATCAGGATTTAGAAGAGGGAGGAACTTAAACGAGAAGTCCTTGAAAAGACTAAGTG
ATGAAACTGGAAATGGAAAACACTTATTTAAGAAAATTAAGAGAAGGAATCAAGCTATCTATTCTACAGAGCATGACAAT
AATTTAGAA

Alignment

ORF - retro_mdom_1119 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 86.93 %
• Parental protein coverage: 64.64 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  KSFFRQEVENNTLGSPAASELLHHLQPTYWFSAHLHVKFAAFMKHQANDGQVPKETKFLALDKCLPHRDF
          KSFF.Q.VENNTLGSPAAS.LLH.LQ.TYWFSAHLHVKFAA.MKHQANDGQ.PKETK.LALDKCLPHRDF
Retrocopy KSFFQQ*VENNTLGSPAASDLLHLLQRTYWFSAHLHVKFAAVMKHQANDGQAPKETKILALDKCLPHRDF

Parental  LQIIEVDHDANAPDYLEYDLEWLTILKATNSLVNVSRSLWNMPENNGLHAKWDYSATEESMKEVLEEMNH
          LQI.EVDHD.NAPDY..YDLEWLTILKATNSLVN.S.SLWNMPENN.L.AKWDYSATEES.KEVLEEMN.
Retrocopy LQILEVDHDVNAPDYFDYDLEWLTILKATNSLVNMS*SLWNMPENNDLQAKWDYSATEESRKEVLEEMNQ

Parental  DLKVPYNFSVTAICYDPSKPQKHMELVHRISPQTTEFCAQLGLTDINNRIQQVIEESSLRGDYEEDVDSN
          DLKVPYNFS.TAI.YDPSKPQKHMELVHRISPQTTE.CAQ.GLTD.NN.IQQVIE.SSL.GDYE.DVD.N
Retrocopy DLKVPYNFSLTAI-YDPSKPQKHMELVHRISPQTTELCAQVGLTDMNNQIQQVIEKSSLCGDYEKDVDNN

Parental  GSEEPSEYNTDNSVLSSSINPDEIMLDEDDEGEDSITGIHGDISTPSVEPSPDHHPPDFSTSFSDIRILP
          GSEEP..YNTDNSVLSSSINPDEIMLDEDDEGED.IT.IHGD.S.PSVEPS.DHH.PDFSTSFSDIRILP
Retrocopy GSEEPRVYNTDNSVLSSSINPDEIMLDEDDEGEDGITVIHGDFSIPSVEPSSDHHLPDFSTSFSDIRILP

Parental  DSMVVSSDGTMNSTNELEKSSENQDSEE-GRNLNEKSLKRLSDETGNGNHLQKKIKRRNQAIYSTEDDNN
          DSMVV.SD.TM.STNELEKS..NQD.EE.GRNLNEKSLKRLSDETGNG.HL.KKIKRRNQAIYSTE.DNN
Retrocopy DSMVVYSDDTMISTNELEKSGKNQDLEE<GRNLNEKSLKRLSDETGNGKHLFKKIKRRNQAIYSTEHDNN

Parental  LE
          LE
Retrocopy LE

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_1119 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_1119 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 1 parental gene, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Monodelphis domestica	ENSMODG00000018554	2 retrocopies	retro_mdom_1119 , retro_mdom_1628,