RetrogeneDB ID: retro_mdom_1021

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 3:245917576..245918425(+)
• Located in intron of: ENSMODG00000020423

Retrocopy information

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

Parental gene information

• Parental gene symbol: CTSZ
• Ensembl ID: ENSMODG00000016601
• Aliases: None
• Description: cathepsin Z [Source:HGNC Symbol;Acc:2547]

Sequence

>retro_mdom_1021
TCTCCTGGTTCTCTGGGATTGCTGGAGAAGGGCCAGAGCTGCTATCGGCCGCTGGAGGGGTTCCAGTCCCGGGAGCACAG
GACCTATCCCAGACCCCATGAATACATGGCATGCTCTAGTCTGCCCAAAGCCTGAGACTGGCGCAACATCAACGGGGTCA
ACTATGCCAGCATCACCCGGAACCAGCACATCCCCCAGTACTGCGGCTCCTGCTGGGCCCACGGCACCACCAGCGCCCTG
GCAGATCGTATCAATATCAAGAGGAAGGGAGCCTGGTCCTCTACGCTCCTGTCTGTGCAACACGTGATTGACTGTGGCAA
TGCTGGGTCCTGTGAGGGTGGCATGGATCTCCCCGTGTGGAAATACGCTCACATGCATGGCATTCCCAATGAGACCTGCA
ACAACTCCCAGGCCAAAGACCAGGAATGTGACAAGTTTAATGAATGTGGTACATGCAATGAATTCCATAATTGCTATTCT
ATAAAGAACTATACTCTCTGGAAAGTTGGAGACTATGGTATCCTTTCTGGGAGAGAAAAAATGATGGCAGAAATATATGC
AAATGGGCCTATCAGTTGTGGCATAATGGCAACGGAAGCCTTGGATAACTACACTGGAGGGATCTATTTTGAATATAATC
CTCAACCTATGATAAACCATATCATTTCTGTGGCTGGGTAGGGTGTTAGTGATAACGGAACAGAATACTGGATTGTCCGA
AATTCATGGGGTGAACCGTGGGGTGAAAAGGGCTGGCTGAGGATTGTAACCAGCAGATATAAAAATGGACAGGATAGTAA
TTACAATCTTGCTATTGAAGAAATGTGTTCATTTGGAGATCCCATAGTT

Alignment

ORF - retro_mdom_1021 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 93.31 %
• Parental protein coverage: 92.51 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  SPSSAGIYYQKGQSCYRPLEGFQSREHRTYPRPHEYMARSSLPKAWDWRNVNGVNYASITRNQHIPQYCG
          SP.S.G....KGQSCYRPLEGFQSREHRTYPRPHEYMA.SSLPKA.DWRN.NGVNYASITRNQHIPQYCG
Retrocopy SPGSLGLL-EKGQSCYRPLEGFQSREHRTYPRPHEYMACSSLPKA*DWRNINGVNYASITRNQHIPQYCG

Parental  SCWAHGTTSALADRINIKRKGAWPSTLLSVQHVIDCGNAGSCEGGMDIPVWEYAHMHGIPDETCNNYQAK
          SCWAHGTTSALADRINIKRKGAW.STLLSVQHVIDCGNAGSCEGGMD.PVW.YAHMHGIP.ETCNN.QAK
Retrocopy SCWAHGTTSALADRINIKRKGAWSSTLLSVQHVIDCGNAGSCEGGMDLPVWKYAHMHGIPNETCNNSQAK

Parental  DQECDKFNECGTCNEFHNCYSIKNYTLWKVGDYGTLSGREKMMAEIYANGPISCGIMATEALDNYTGGIY
          DQECDKFNECGTCNEFHNCYSIKNYTLWKVGDYG.LSGREKMMAEIYANGPISCGIMATEALDNYTGGIY
Retrocopy DQECDKFNECGTCNEFHNCYSIKNYTLWKVGDYGILSGREKMMAEIYANGPISCGIMATEALDNYTGGIY

Parental  FEYNPQPMINHIISVAGWGVSDNGTEYWIVRNSWGEPWGEKGWLRIVTSRYKDGQGSNYNLAIEETCSFG
          FEYNPQPMINHIISVAG.GVSDNGTEYWIVRNSWGEPWGEKGWLRIVTSRYK.GQ.SNYNLAIEE.CSFG
Retrocopy FEYNPQPMINHIISVAG*GVSDNGTEYWIVRNSWGEPWGEKGWLRIVTSRYKNGQDSNYNLAIEEMCSFG

Parental  DPIV
          DPIV
Retrocopy DPIV

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	15.85 RPM
SRP007412_cerebellum	0.00 RPM	9.47 RPM
SRP007412_heart	0.00 RPM	24.92 RPM
SRP007412_kidney	0.00 RPM	31.60 RPM
SRP007412_liver	0.00 RPM	295.55 RPM
SRP007412_testis	0.00 RPM	8.45 RPM

ChIP-Seq

Monodelphis domestica was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mdom_1021 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_1021 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 5 parental genes, and 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Dasypus novemcinctus	ENSDNOG00000012612	1 retrocopy	retro_dnov_2521,
Felis catus	ENSFCAG00000000845	1 retrocopy	retro_fcat_383,
Monodelphis domestica	ENSMODG00000002844	1 retrocopy	retro_mdom_1101,
Monodelphis domestica	ENSMODG00000012029	6 retrocopies	retro_mdom_1066, retro_mdom_1067, retro_mdom_1199, retro_mdom_1707, retro_mdom_1973, retro_mdom_1985,
Monodelphis domestica	ENSMODG00000016601	1 retrocopy	retro_mdom_1021 ,