RetrogeneDB ID: retro_mdom_683

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 2:92662543..92663896(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSMODG00000000608
• Aliases: None
• Description: None

Sequence

>retro_mdom_683
ACACACAAAACTACCTCCCAGAGAAAGACTTGTCCCCTTTTATTCCCCAAATACTCAATTTTGAGTATGGTAGAGGAAGG
TGTGCTGTTATCACATTTGATGAGTAGTAATATACATGAAATGAATTATGATTTGTTATGTGAACTCTACAGAATATCTA
CATACTCTGCTTTCCCAGTCAATGTTCCAATCTCAGAAAGGAGTCTTGCTCGGGCTGGATTTTATTACACTGGTATGAAT
GACAGAGTTAAATGTTTCTGTTGTGGCTTAATGCTGGATAACTGGAAACAAGGGGACAATGCGATTGACAAACATAAACA
GCTATATCCTAGCTGTGCCTTTATTCAGAATTTGATTTCAGTTAATCTGGGATCTTCTCAGTCTACATTTTCTTCTTCAG
TGAATAATGCCACACGTTCATTATCTCTCAGTTCAGAACAGAGTGGATATTTCAGTGGTTCTTATTCCAGTTTTCCACTG
GAGCCAGTGACTTCCAGAGGAGTTGAGGACTTGTCCCCTTTGAATATCAGCCCCTACAGTTATTCTATGAGTACTGAAGA
GGCCAGAATTCTTACTTACCAGGCATGGCCATTGACATTTCTGTCATCATTAGATCTGGTAAGAGCTGGCTTTTATTATA
TAGGACCTGGAGACATGGTAGCTTGCTTTGCCTGTGGTGGGAAACTGAGTAACTGGGAACTAAAAGATGATGCCATGTCA
GAGCACTGAAGACATTTTCCTCACTGTCCTTTCCTGGAGAGTCAAATCCAAGAAACATCAAGATTCAATGTTTCTAATGT
GAGCATGCAAACCCATGCAGCCCGTGTGAAAACCTTTGTGACCTGGCCACCTCAAATTCCAGTTCATCCAGAGCAGCTTG
CAAGTGCTGGCTTTTATTATGTGGGTCGAAATGATGATGTGAAGTGCTTTTGCTGTGATGGTGGACTGAGATGTTGGGAA
TCCAGAGATGATCCTTGGGTGGAACATGCCAAATGGTTCCCAAGGTGTGAGTACTTGATACGAATGAAAGGTCAAGAGTT
TGTTGACCAAGTTCAAGCTAGGTACCCTCATCTCCTTGAACAGGTATTATCAACTTCAGATATTCCAGGAGATGAAAATG
TTGAACTACCAATTATTCATTTGGAGCCTGGAAAAAATAATTCACAAGATATAGTCCTGATGAACACTCCAGTGATTAAA
GCTGCTTTGGAAATGGGCTTCAGTAGAAGTCTAGTAAAACAGATTGTTCAGAGTAAAATCTTAACTACTGGAGAAAATTA
CAAAACAGTCAATGAGGTTGTATTGGATCTCCTCAATGCAGAAGATGAAAAAAGGAAAGAGGAGAGAGACAAA

Alignment

ORF - retro_mdom_683 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 93.13 %
• Parental protein coverage: 72.58 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  THKTTSQRKTCPLLFPKYSIMSVVEDGVLLSHLMSSDTHEMKYDLSCELYRMSTYSAFPVNVPISERSLA
          THKTTSQRKTCPLLFPKYSI.S.VE.GVLLSHLMSS..HEM.YDL.CELYR.STYSAFPVNVPISERSLA
Retrocopy THKTTSQRKTCPLLFPKYSILSMVEEGVLLSHLMSSNIHEMNYDLLCELYRISTYSAFPVNVPISERSLA

Parental  RAGFYYTGVNDRVKCFCCGLMLDNWKQGDNAIDKHKQLYPSCAFIQNLISVNLGSSQSTFSSSVNNATRS
          RAGFYYTG.NDRVKCFCCGLMLDNWKQGDNAIDKHKQLYPSCAFIQNLISVNLGSSQSTFSSSVNNATRS
Retrocopy RAGFYYTGMNDRVKCFCCGLMLDNWKQGDNAIDKHKQLYPSCAFIQNLISVNLGSSQSTFSSSVNNATRS

Parental  LSLSSEQSGYFSGSYSSFPLEPVTSRGVEDLSPLNTSPYSYSMSTEEARILTYQAWPLTFLSPLDLARAG
          LSLSSEQSGYFSGSYSSFPLEPVTSRGVEDLSPLN.SPYSYSMSTEEARILTYQAWPLTFLS.LDL.RAG
Retrocopy LSLSSEQSGYFSGSYSSFPLEPVTSRGVEDLSPLNISPYSYSMSTEEARILTYQAWPLTFLSSLDLVRAG

Parental  FYYIGPGDMVACFACGGKLSNWEPKDDAMSEHRRHFPHCPFLESQIQETSRFNVSNLSMQTHAARVKTFV
          FYYIGPGDMVACFACGGKLSNWE.KDDAMSEH.RHFPHCPFLESQIQETSRFNVSN.SMQTHAARVKTFV
Retrocopy FYYIGPGDMVACFACGGKLSNWELKDDAMSEH*RHFPHCPFLESQIQETSRFNVSNVSMQTHAARVKTFV

Parental  TWPPQIPVHPEQLANAGFYYVGRNDDVKCFCCDGGLRCWESGDDPWVEHAKWFPR-QYLIRMKGQEFVDQ
          TWPPQIPVHPEQLA.AGFYYVGRNDDVKCFCCDGGLRCWES.DDPWVEHAKWFPR..YLIRMKGQEFVDQ
Retrocopy TWPPQIPVHPEQLASAGFYYVGRNDDVKCFCCDGGLRCWESRDDPWVEHAKWFPRCEYLIRMKGQEFVDQ

Parental  VQARYPHLLEQLLSTSDIPGDENAELPIIHFGPGENNSEDTVMMNTPVIKAALEMGFSRSLVKQIVQSKI
          VQARYPHLLEQ.LSTSDIPGDEN.ELPIIH..PG.NNS.D.V.MNTPVIKAALEMGFSRSLVKQIVQSKI
Retrocopy VQARYPHLLEQVLSTSDIPGDENVELPIIHLEPGKNNSQDIVLMNTPVIKAALEMGFSRSLVKQIVQSKI

Parental  LTTGENYKTVNEVVSDLLNAEDEKRKEEKER
          LTTGENYKTVNEVV.DLLNAEDEKRKEE...
Retrocopy LTTGENYKTVNEVVLDLLNAEDEKRKEERDK

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_683 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_683 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 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000035735	1 retrocopy	retro_btau_1262,
Monodelphis domestica	ENSMODG00000000608	3 retrocopies	retro_mdom_1857, retro_mdom_585, retro_mdom_683 ,
Otolemur garnettii	ENSOGAG00000010377	2 retrocopies	retro_ogar_2542, retro_ogar_953,
Otolemur garnettii	ENSOGAG00000030385	1 retrocopy	retro_ogar_3331,
Ictidomys tridecemlineatus	ENSSTOG00000005734	1 retrocopy	retro_itri_426,