RetrogeneDB ID: retro_mdom_877

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 2:263759593..263760229(-)
• Located in intron of: ENSMODG00000007372

Retrocopy information

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

Parental gene information

• Parental gene symbol: GATAD1
• Ensembl ID: ENSMODG00000010701
• Aliases: None
• Description: GATA zinc finger domain containing 1 [Source:HGNC Symbol;Acc:29941]

Sequence

>retro_mdom_877
GGTGGGCCGGGCTCCGGCTTCGCCGGCAACTTGGCAGAGGCCTCTCATCAGAGCAATGGTGGCGGGGATGGCGGGGGCGG
CAAGCAGGAGATACACCGGCGCTCGGCGCGCCTGCGGAATACCAAGTACAAGTCAGCCCCGGCGGCTGAGAAGAAGGAGT
CCACCAAGGGCAAGGGCCGCAGGCACATTTTTAAGCTGAAGAACCCTATCAAAGCTCCTGAAGCAGTTTCCACTATCATT
ACTGCAGAATCAATATTTCACAAGGGAATGTACTATCAGATCGGAGATGTTGTTTCTGTAGTTGATGAACAAGATGGAAA
AACATACTATGCGCAAATAAGGGGCTTTATCCAGGACCAGTACTGTGAGAAGAGTGCGGCACTAACTTGGCTCATCCTCA
CATTGGCCAGCCCCAAAGACCAGTTTGACCCAGCGTCTTATATCATAGGACCAGAAGAAGACCTTCCAAGGAAGATGGAA
TATTTGGAATTTGTTTGCCATGCACCTTCAGAATATTTCAAGTCTCGATCCTCACCATTCCCCACTGTTCCCACTAGACC
AGAGAATGGGTACATATGGACTCATGTTGGACCTACTCCTGCCATTACCATTAAGGAAACAGTTGCCAACAACTTG

Alignment

ORF - retro_mdom_877 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 89.67 %
• Parental protein coverage: 78.89 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  GGGGTPGAGAGTAGGGGAPGGGHGGRQSKQEIHRRSARLRNTKYKSAPAAEKKVSTKGKGRRHIFKLKNP
          GG.G...AG..........GGG.GG...KQEIHRRSARLRNTKYKSAPAAEKK.STKGKGRRHIFKLKNP
Retrocopy GGPGSGFAGNLAEASHQSNGGGDGGG-GKQEIHRRSARLRNTKYKSAPAAEKKESTKGKGRRHIFKLKNP

Parental  IKAPEAVSTIITAESIFHKGVYYQIGDVVSVVDEQDGKTYYAQIRGFIQDQYCEKSAALTWLIPTLASPK
          IKAPEAVSTIITAESIFHKG.YYQIGDVVSVVDEQDGKTYYAQIRGFIQDQYCEKSAALTWLI.TLASPK
Retrocopy IKAPEAVSTIITAESIFHKGMYYQIGDVVSVVDEQDGKTYYAQIRGFIQDQYCEKSAALTWLILTLASPK

Parental  DQFDPASYIIGPEEDLPRKMEYLEFVCHAPSEYFKSRSSPFPTVPTRPEKGYIWTHVGPTPAITIKETVA
          DQFDPASYIIGPEEDLPRKMEYLEFVCHAPSEYFKSRSSPFPTVPTRPE.GYIWTHVGPTPAITIKETVA
Retrocopy DQFDPASYIIGPEEDLPRKMEYLEFVCHAPSEYFKSRSSPFPTVPTRPENGYIWTHVGPTPAITIKETVA

Parental  NNL
          NNL
Retrocopy NNL

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_877 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_877 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 4 parental genes, and 14 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000000193	2 retrocopies	retro_chof_2074, retro_chof_2604,
Dipodomys ordii	ENSDORG00000005895	10 retrocopies	retro_dord_267, retro_dord_270, retro_dord_300, retro_dord_318, retro_dord_363, retro_dord_459, retro_dord_463, retro_dord_504, retro_dord_551, retro_dord_566,
Monodelphis domestica	ENSMODG00000010701	1 retrocopy	retro_mdom_877 ,
Oryctolagus cuniculus	ENSOCUG00000014806	1 retrocopy	retro_ocun_1772,