RetrogeneDB ID: retro_mdom_770

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 2:402312606..402313144(+)
• Located in intron of: ENSMODG00000017651

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSMODG00000025406
• Aliases: None
• Description: None

Sequence

>retro_mdom_770
CTAGAAAACAGATCCAGAAGAGACAATTTAAGAATAATTGGACTACCAGATTATCATGACAATAGAAAAAACCTGGGCAA
CATTCTACAGGAAATTATCCAAGGAACTTGCCCCAACATACTAGAGCAAGAGGGAAAGATAGAGATCAACTCCAGTACCT
AATCCCCAACTGACAATACCCAGGAATGTTATAGCCAAATTCAAGAACTTCTAGGACAAAGAAAAAATATTATAAGCTGC
TAAAAGGAAGTCATTCAGATATCATGGAACAACAGTTAGGATAACATAAATTCTGGCTTCATTTGCACAAAATGACCAAA
AGGCATGGAATATGGTTTTCCAGAAAGCAAAGGAACTAGGTCTCCAACCAAAAAATCAACTACCCTTAAAAACTGACTGT
ATTCTTACAAGGGAAAATATGGTCATTTAATAAAATAGAATTCCAAGTATTTGTAAAAAACAGACCAGAACTGAACAGAA
AATCTGGTGCCCAAACACAGAACTCAAGAGACTCATCAAGAGGTAATTAAGAAGGGGG

Alignment

ORF - retro_mdom_770 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 62.16 %
• Parental protein coverage: 57.46 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  LENRSRRDNLRIIGLPEDHDKRKSLDIMLQEIIK-ENFPNILEQEGINT-RSHPVLNPQLTTARNVIAKF
          LENRSRRDNLRIIGLP..HD.RK.L...LQEII...N.P......G....RS.PV.NPQLT..RNVIAKF
Retrocopy LENRSRRDNLRIIGLPDYHDNRKNLGNILQEIIQ<RNLPQHTRARGKDR<RSTPVPNPQLTIPRNVIAKF

Parental  KNYQTKEKILQAAKKKSFRYHGTTVRITQDLAASTLKHRKARKNIIHTQRKNCLQP-RINYPAKLTIFLQ
          KN...KEKIL.AAK.KSFRYHGTTVRIT..LA.......KA............LQP..INYP.KLT.FLQ
Retrocopy KNF*DKEKIL*AAKRKSFRYHGTTVRIT*ILASFAQNDQKAWNMVFQKAKELGLQP>KINYP*KLTVFLQ

Parental  GKVWSFNKIEEFQEFVKKRPHLIRKFDVQAQNSRESSKDN-LKRG
          GK.WSFNKI.EFQ.FVK.RP.L.RK...Q.QNSR.SS..N.L.RG
Retrocopy GKIWSFNKI-EFQVFVKNRPELNRKSGAQTQNSRDSSRGN<LRRG

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_770 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_770 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.

---

Parental genes homology:

Parental genes homology involve 1 parental gene, and 12 retrocopies.

Species	Parental gene accession	Retrocopies number
Monodelphis domestica	ENSMODG00000025406	12 retrocopies	retro_mdom_1000, retro_mdom_1578, retro_mdom_1642, retro_mdom_1712, retro_mdom_1767, retro_mdom_1795, retro_mdom_2008, retro_mdom_502, retro_mdom_770 , retro_mdom_842, retro_mdom_900, retro_mdom_972,