RetrogeneDB ID: retro_mdom_1463

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 5:177599854..177600781(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMODG00000020595
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSMODG00000020916
• Aliases: None
• Description: None

Sequence

>retro_mdom_1463
CATGACAACCTTTTTGACAAAGTGAGAGAAATGTGTAGTTTACAGCAGTAGCAGCCAATCACCCTCAAATGTATTGATGA
TGAAGGTGACCCATACAACATATTGTCTCAGATGGAACTGGAAGAAGCATTTCATCTGTAGTGTCAACACAGATATGAAA
GACTCATCATTCATGTTTTTCCAAGCATCCCAGCGAAGCCATGAATGCCCTATCCAGGAGAAGACAAATCAATTGACTGC
TGTGGTGCCAGAAGATGGAGGAAACCCTACCAAGTGAATGGGCATCTGTTTCAAGCCAAATATTTCAACAGAAGAGCATA
CTGTGGCCAGTGCAATGAAAGGATATGGGGTCTCGGAAGGCAAGGCTAAAAGTATATCAGCTTCAAATTACTGGTCTATA
AATCTTGTCATATACTTGTACCACTGACCTGCAAAAGGAATATGGATTTGGTGATGCCTTCCTAAGAACCTCAAATAGAT
GATATAAACAATGAAGCTGACCTTCCCTCCAAAAAAAATGATGGGCTTGTTTATATTCCCTCAACCCTGAAACATGACAG
TTTTAAAGACGATTCTGAGGACATTAAGCTAGTTATCGATGGAATGGATGGAATAAAAATATACCAGGGGCTCGGGCTGC
AGGACTTCAATTTAATCAGAGATATTGGATGGGGCATTATGCCAAAGCTCTCTTAGTGCGATTGAAAAAGAATGACCAGA
TTTAAGCTGTGAAGGTAGTAAAAAAGGAGTTGGTCCATGATGATGAAAATATTGACTGGCTGCAGATAGATAAGCATGTT
TTTGAACAGGCCTCCAGTAACCTTCCTTGTTGGCCTACACTCCTGCTTCCAAACAACAAGTCAGTTATTGCTTGTCATGG
AGTATGTGAATGGAGGAGATTTCATGTTTCATATGCAAATGCAAAGA

Alignment

ORF - retro_mdom_1463 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 78.73 %
• Parental protein coverage: 54.74 %
• Number of stop codons detected: 6
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  YDELCDEVREMCSLQQHQPITLKWIDDEGDPCTISSQMELEEAFRLYCQHRDEGLIIHGKFFPSIPEKPG
          .D.L.D.VREMCSLQQ.QPITLK.IDDEGDP..I.SQMELEEAF.L.CQHR.E.LIIH...FPSIP.KP.
Retrocopy HDNLFDKVREMCSLQQ*QPITLKCIDDEGDPYNILSQMELEEAFHL*CQHRYERLIIH--VFPSIPAKP*

Parental  MPCPGEDKSIYRRGARRWRKLYRVNGHLFQAKRFNRRAYCGQCSERIWGLGRQGYKCINCKLLVHKRCHI
          MP.PGEDKSI...GARRWRK.Y.VNGHLFQAK.FNRRAYCGQC.ERIWGLGRQG.K.I..KLLV.K.CHI
Retrocopy MPYPGEDKSIDCCGARRWRKPYQVNGHLFQAKYFNRRAYCGQCNERIWGLGRQG*KYISFKLLVYKSCHI

Parental  LVPLTCKRHMDSVMPSQEPQIDDKNDEVDLPSEENDGLAYIPSTRKHDSLKDDSEDIKPVIDGMDGIKIS
          LVPLTCKR.MD.VMPS.EPQIDD.N.E.DLPS...DGL.YIPST.KHDS.KDDSEDIK.VIDGMDGIKI.
Retrocopy LVPLTCKRNMDLVMPS*EPQIDDINNEADLPSXXXDGLVYIPSTLKHDSFKDDSEDIKLVIDGMDGIKIY

Parental  QGLGLQDFDLIRVIG-RGSYAKVLLVRLKKNDQIYAMKVVKKELVHDDEDIDWVQTEKHVFEQASSN-PF
          QGLGLQDF.LIR.IG..G.YAK.LLVRLKKNDQI.A.KVVKKELVHDDE.IDW.Q..KHVFEQASSN.P.
Retrocopy QGLGLQDFNLIRDIG<MGHYAKALLVRLKKNDQI*AVKVVKKELVHDDENIDWLQIDKHVFEQASSN<PS

Parental  LV-GLHSCFQTTSRLFLVIEYVNGGDLMFHMQRQR
          L..GLHSCFQTTS.L.LV.EYVNGGD.MFHMQ.QR
Retrocopy LL<GLHSCFQTTSQLLLVMEYVNGGDFMFHMQMQR

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_1463 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_1463 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 2 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Monodelphis domestica	ENSMODG00000020916	3 retrocopies	retro_mdom_1158, retro_mdom_1336, retro_mdom_1463 ,
Mus musculus	ENSMUSG00000029053	1 retrocopy	retro_mmus_3013,