RetrogeneDB ID: retro_mdom_1225

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 4:21823908..21824530(+)
• Located in intron of: ENSMODG00000021095

Retrocopy information

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

Parental gene information

• Parental gene symbol: PTPN2
• Ensembl ID: ENSMODG00000021422
• Aliases: None
• Description: protein tyrosine phosphatase, non-receptor type 2 [Source:HGNC Symbol;Acc:9650]

Sequence

>retro_mdom_1225
GACTCAGTAAAATGTGCACAACATTGGCCAACCAAAGAAGACCAAGTGATGGTGTTTGAAGAGACAGGATTCTGTGTGAG
ACTAGTGTCCGAAGATTTCAAATCATATCATACACTTCATGTATTAAAATTAGAAAATATTCATAGTGGTGAGTTCAGCA
TAATATCTCACTTTTATTATACTCTGTGGCCAGATTTTGGAGTCCCTCAATCACCAGCTTCATTCCTCAACTTCTTATTT
AAAGTTCAAGAATCTGGTTCCCTGAATGCTGAACATGGGCCTGCAATAATTCACTGTAGTGCAGGTATTGGCCAGTCTGG
CACATTTTCATTAGTTGATACTTGTTTTGTCCTGATGGAAAAAGAGATGATCTTTTTTGCTTAATTTTATGCAAGTATTA
GTGAAAATGAGAAAATTTCAAATGGGACTTATTCAGACTCCAGATCAACTAAGATTTTCATGTATGGCTGTAATACAAAA
AGCAAAATTTATAATGGGAGATTCATATATACCTAAGTGTTGGAAAGAACTCTCTAAGGAAGACAAGGCACCTAACTATG
AACATTCCCCACCTCATCCAAATAGAATAATTACTGGAAAGTGAGATGGGAATAGTGTGAAA

Alignment

ORF - retro_mdom_1225 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 79.52 %
• Parental protein coverage: 52.66 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  DSIKCAQYWPTKEDKVMVFEETGFCVRLVSEDVKSYYTVHLLKLENLHSGEIRLISHFHYTTWPDFGVPQ
          DS.KCAQ.WPTKED.VMVFEETGFCVRLVSED.KSY.T.H.LKLEN.HSGE...ISHF.YT.WPDFGVPQ
Retrocopy DSVKCAQHWPTKEDQVMVFEETGFCVRLVSEDFKSYHTLHVLKLENIHSGEFSIISHFYYTLWPDFGVPQ

Parental  SPASFLNFLFKVRESGSLSDEHGPAIIHCSAGIGRSGTFSLVDTCLVLME-KRDD-PFSVNIKQVLVNMR
          SPASFLNFLFKV.ESGSL..EHGPAIIHCSAGIG.SGTFSLVDTC.VLME.KRDD..F..N..QVLV.MR
Retrocopy SPASFLNFLFKVQESGSLNAEHGPAIIHCSAGIGQSGTFSLVDTCFVLME<KRDD<SFLLNFMQVLVKMR

Parental  KFRMGLIQTPDQLRFSYMAVIEGAKFIMGDSNIQKRWKELSNEDEAPNYEHSPPHPTKIIPGKYNGNRLE
          KF.MGLIQTPDQLRFS.MAVI..AKFIMGDS.I.K.WKELS.ED.APNYEHSPPHP..II.GK..GN...
Retrocopy KFQMGLIQTPDQLRFSCMAVIQKAKFIMGDSYIPKCWKELSKEDKAPNYEHSPPHPNRIITGK*DGNSVK

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_1225 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_1225 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 15 parental genes, and 23 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000000867	1 retrocopy	retro_chof_2231,
Callithrix jacchus	ENSCJAG00000005102	1 retrocopy	retro_cjac_1577,
Dasypus novemcinctus	ENSDNOG00000016588	1 retrocopy	retro_dnov_1466,
Erinaceus europaeus	ENSEEUG00000005636	1 retrocopy	retro_eeur_370,
Echinops telfairi	ENSETEG00000005577	2 retrocopies	retro_etel_1743, retro_etel_1942,
Homo sapiens	ENSG00000175354	2 retrocopies	retro_hsap_1186, retro_hsap_480,
Gorilla gorilla	ENSGGOG00000010259	2 retrocopies	retro_ggor_453, retro_ggor_925,
Loxodonta africana	ENSLAFG00000011818	1 retrocopy	retro_lafr_701,
Macropus eugenii	ENSMEUG00000005156	1 retrocopy	retro_meug_653,
Monodelphis domestica	ENSMODG00000003120	1 retrocopy	retro_mdom_516,
Monodelphis domestica	ENSMODG00000021422	1 retrocopy	retro_mdom_1225 ,
Nomascus leucogenys	ENSNLEG00000009074	3 retrocopies	retro_nleu_2112, retro_nleu_351, retro_nleu_894,
Otolemur garnettii	ENSOGAG00000028605	1 retrocopy	retro_ogar_3429,
Pongo abelii	ENSPPYG00000008983	3 retrocopies	retro_pabe_1077, retro_pabe_1144, retro_pabe_989,
Pan troglodytes	ENSPTRG00000009884	2 retrocopies	retro_ptro_361, retro_ptro_813,