RetrogeneDB ID: retro_mdom_1986

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: Un:70784642..70785721(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CFLAR
• Ensembl ID: ENSMODG00000015097
• Aliases: None
• Description: CASP8 and FADD-like apoptosis regulator [Source:HGNC Symbol;Acc:1876]

Sequence

>retro_mdom_1986
CTAGGAGGAGGGAAGCCTACAAGAACAAGAGTTTCTTAGATGTTGTTATCGAATTAGAGAAGGTAAACCTGATTTCTCCT
GACAAGTTAGATTTACTGGAAAAATGTCTGAAGAATATTCACAGGATTGATTTGAAGAAAAAAATTCAGAAATATAAACA
GTCAGCTTTGGAAGCAAACTATGTAAATGGAATCCCGACTTCCCTGCCAGCTGTAAGCCTGAGAGATCCTGTTTATGGCT
TAATGCTCAAGAATGGGATAAAAAAGGAAGAAAGGCCAACCTTTGGACAACGTGGAATTTCAACTGAACCACTTAAACTA
TCCATTCAGGAATCCAGAAAATCCTTGCCTCAGATGGCTGACGACATATACAGGCTAAGGAGTCAACCATTGGGCGTTTG
TTTAATAATTGATTGCATTGGCAATGATGCAGAGACACTTACGGCCACATTTACTTCCCTGGGGTTTGAAGTTCAGTGTC
ACCAATGCCTGCGCACGGAAGAAATCCACAAGACCCTTGGCCAAGTTGCCTGTCTCACCACGCATCAGGACTATGACATT
TTTGTGTGTATTGTGATCAGTCGAGGTAACTCCGAGGGGATTTTTGGAGTAAACCACCAGACTTACCCAGTATTCCCTCT
GCAGCAGATCAAGAAGCCTTTCACTGGGGATGCCTGCCCTTTTCTCTCAGGGAAACCCAAACTCTTTTTTATTCAGAACT
ATATGGTAGCAGAAGACCAGCAAGAATCAAATAATGTCTTGGAGGTGGATGGGGATGGCGGCAAAGGGTCTTATCTGAGG
CAGAGACCTGGAGGGTCATCTGTGCCTCAGGAAGCCGACATTTTTTGGAGCGTGTGCACCGTGAATGTTTCTGTGCTGGA
GAGATACCCCAATTCACCATCCTTCTACCTGCGTTCCCTGTCACAGCTCCTGCGTCGACCTGAAGAGAGAAGGTGCTCGC
TTTTGAGTCTCCACATTGATCTCAACAACAAAATCTTTGACTGGAATAGCAGAGTGATTCCTGAAGAGCAGTACTCTATC
CTATTAGAACATACTCTGAGGAAGAAAATTGTTCTTTCC

Alignment

ORF - retro_mdom_1986 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 98.07 %
• Parental protein coverage: 70.59 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  IGGGKP-YKNKKHFLDVVIELEKVNLISPDKLDLLEKCLKNIHRIDLKKKIQKYKQSALEANYVNGIPTS
          .GGGKP.YKNK..FLDVVIELEKVNLISPDKLDLLEKCLKNIHRIDLKKKIQKYKQSALEANYVNGIPTS
Retrocopy LGGGKP<YKNKS-FLDVVIELEKVNLISPDKLDLLEKCLKNIHRIDLKKKIQKYKQSALEANYVNGIPTS

Parental  LPAVNLRDPVYGLMLKNGIKKEERPTFGQRGISTEPLKLSIQESRKSLPQMADDIYRLRSQPLGVCLIID
          LPAV.LRDPVYGLMLKNGIKKEERPTFGQRGISTEPLKLSIQESRKSLPQMADDIYRLRSQPLGVCLIID
Retrocopy LPAVSLRDPVYGLMLKNGIKKEERPTFGQRGISTEPLKLSIQESRKSLPQMADDIYRLRSQPLGVCLIID

Parental  CIGNDAETLTATFTSLGFEVQCHQCLRTEEIHKTLGQVACLTTHQDYDIFVCIVISRGNSEGIFGVNHQT
          CIGNDAETLTATFTSLGFEVQCHQCLRTEEIHKTLGQVACLTTHQDYDIFVCIVISRGNSEGIFGVNHQT
Retrocopy CIGNDAETLTATFTSLGFEVQCHQCLRTEEIHKTLGQVACLTTHQDYDIFVCIVISRGNSEGIFGVNHQT

Parental  YPVFPLQQIKKPFTGDACPFLSGKPKLFFIQNYMVAEDQQESNNVLEVDGDGGKGSYLGQRPGGSSVPQE
          YPVFPLQQIKKPFTGDACPFLSGKPKLFFIQNYMVAEDQQESNNVLEVDGDGGKGSYL.QRPGGSSVPQE
Retrocopy YPVFPLQQIKKPFTGDACPFLSGKPKLFFIQNYMVAEDQQESNNVLEVDGDGGKGSYLRQRPGGSSVPQE

Parental  ADIFWSVCTVNVSVLERYPNSPSFYLRSLSQLLRRPEE-RCSLLSLHIDLNNKIFDWNSRVIPEEQYSIL
          ADIFWSVCTVNVSVLERYPNSPSFYLRSLSQLLRRPEE.RCSLLSLHIDLNNKIFDWNSRVIPEEQYSIL
Retrocopy ADIFWSVCTVNVSVLERYPNSPSFYLRSLSQLLRRPEERRCSLLSLHIDLNNKIFDWNSRVIPEEQYSIL

Parental  LEHTLRKKIVLS
          LEHTLRKKIVLS
Retrocopy LEHTLRKKIVLS

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_1986 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_1986 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 3 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000004505	1 retrocopy	retro_cjac_3235,
Monodelphis domestica	ENSMODG00000015097	1 retrocopy	retro_mdom_1986 ,
Mus musculus	ENSMUSG00000026031	1 retrocopy	retro_mmus_244,