RetrogeneDB ID: retro_mdom_1973

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: Un:20723301..20724311(-)
• Located in intron of: ENSMODG00000029193

Retrocopy information

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

Parental gene information

• Parental gene symbol: CTSB
• Ensembl ID: ENSMODG00000012029
• Aliases: None
• Description: cathepsin B [Source:HGNC Symbol;Acc:2527]

Sequence

>retro_mdom_1973
ATGTGGTGGTTCTTGGCCACCCTGTGTTGCCTGGTCGTACTGACCAGTGCCAAGAGCAGATTATCCTTTCCTCCTCTATC
AGATGAAATGGTCAACCACATCAACAAGCTCAACACTGCATGGCAGGCTGCGCACAACTTCCTTAATGCAGACATGAGCT
ACATAAAGAAACTCTGTGGTACCTTCATGTGTGGAGCCAAGCTACTACCTTAGAGAATGATAATGGCTGATAATATGAAG
CTACCAGAAAACTTTGATGCCTGGGAACAATGGCCAAACTGCCCTACTATCAAGGAAATAAGAGACCAGGGTTCCTGTGG
ATCTTGCTGGGCATTTGGAGCTGTGGAAGCTGTTTCTGACAGGATCTGTGTACACAGTAATGGAAATGCTAATGTAGAAG
TGTCTGCTGAGGATCTCCTTAGCTGCTGTGGATCTGAATGTGGGGATGGCTGTAATGGCGGTTTTCCTGCTGGAGCTTGG
AACTTCTGGACTAAGAAAGGCCTTGTATCTGGTGGTCTCTATGATTCCCATGTGGGCTGCTGACCTTATTCCATCCCTCC
ATGTGAGCACCATGTGAATGGCTCCCATTCTGCCTGTACTGGAGAAGAGGGCGACACCCCCAGGTGCAGGAAGAAGTGTG
AAGAGGGCTATTCTACTCAGTACAAGGATGACAAAAACTACAGATCAACCCCCTATAGGGTACGTTCAAGTGAGCAGGAG
ATCATGGCTGAGATCTACAAGAATGGCCCTGTGGAGGGAGCTTTTAGTGTGTATGAAGACTTCCTACACTACAAGTCTGG
AGTATACCAGCACGTTGCTGGAGAGATGCTTGGAGGTCACGCCATTCAAATCCTGGCTGGGGTGTGGAAAATGGAATCCG
TTACTGGCTGGCTGCCAACTCCTGGAATATTGACTGGGGTGATAATGGCTTCTTTAAATTCCTCCGTGGAAAGAATCACT
GTGGGATAGAATCTGAAATTGTGGCTGGAATTCCCAGAACGGATCAATAT

Alignment

ORF - retro_mdom_1973 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 93.79 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MWRFLATLCCLVVLTSAKSRLSIPPLSDEMVNHINKLNTTWQAGHNFLNADMSYVKKLCGTFMGGAKLLP
          MW.FLATLCCLVVLTSAKSRLS.PPLSDEMVNHINKLNT.WQA.HNFLNADMSY.KKLCGTFM.GAKLLP
Retrocopy MWWFLATLCCLVVLTSAKSRLSFPPLSDEMVNHINKLNTAWQAAHNFLNADMSYIKKLCGTFMCGAKLLP

Parental  QRMILADNMKLPENFDAREQWPNCPTIKEIRDQGSCGSCWAFGAVEAISDRICVHSNGNANVEVSAEDLL
          .RMI.ADNMKLPENFDA.EQWPNCPTIKEIRDQGSCGSCWAFGAVEA.SDRICVHSNGNANVEVSAEDLL
Retrocopy *RMIMADNMKLPENFDAWEQWPNCPTIKEIRDQGSCGSCWAFGAVEAVSDRICVHSNGNANVEVSAEDLL

Parental  SCCGSECGDGCNGGFPAGAWNFWTKKGLVSGGLYDSHVGCRPYSIPPCEHHVNGSRPACTGEEGDTPTCR
          SCCGSECGDGCNGGFPAGAWNFWTKKGLVSGGLYDSHVGC.PYSIPPCEHHVNGS..ACTGEEGDTP.CR
Retrocopy SCCGSECGDGCNGGFPAGAWNFWTKKGLVSGGLYDSHVGC*PYSIPPCEHHVNGSHSACTGEEGDTPRCR

Parental  KKCEEGYSTQYKDDKNYGSTSYSVPSSEQEIMAEIYKNGPVEGAFSVYEDFLHYKSGVYQHVAGEMLGGH
          KKCEEGYSTQYKDDKNY.ST.Y.V.SSEQEIMAEIYKNGPVEGAFSVYEDFLHYKSGVYQHVAGEMLGGH
Retrocopy KKCEEGYSTQYKDDKNYRSTPYRVRSSEQEIMAEIYKNGPVEGAFSVYEDFLHYKSGVYQHVAGEMLGGH

Parental  AIRIL-GWGVENGIRYWLAANSWNIDWGDNGFFKFLRGKNHCGIESEIIAGIPRTDQY
          AI.IL.GWGVENGIRYWLAANSWNIDWGDNGFFKFLRGKNHCGIESEI.AGIPRTDQY
Retrocopy AIQIL<GWGVENGIRYWLAANSWNIDWGDNGFFKFLRGKNHCGIESEIVAGIPRTDQY

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	914.00 RPM
SRP007412_cerebellum	0.00 RPM	672.82 RPM
SRP007412_heart	0.00 RPM	697.33 RPM
SRP007412_kidney	0.00 RPM	1077.17 RPM
SRP007412_liver	0.00 RPM	2749.05 RPM
SRP007412_testis	0.00 RPM	434.90 RPM

ChIP-Seq

Monodelphis domestica was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mdom_1973 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_1973 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 6 parental genes, and 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000164733	1 retrocopy	retro_hsap_3032,
Loxodonta africana	ENSLAFG00000007380	1 retrocopy	retro_lafr_1150,
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,
Mus musculus	ENSMUSG00000021939	1 retrocopy	retro_mmus_1921,