RetrogeneDB ID: retro_ogar_3429

Retrocopy location

• Organism: Bushbaby (Otolemur garnettii)
• Coordinates: GL873832.1:488669..489384(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PTPN2
• Ensembl ID: ENSOGAG00000028605
• Aliases: None
• Description: protein tyrosine phosphatase, non-receptor type 2 [Source:HGNC Symbol;Acc:9650]

Sequence

>retro_ogar_3429
AGAAATTGAAGCCCATATGATCACAGTCACATTAAACTGCAAAATACAGCAAATGATTATATTAATGCCCCTGAGTTGAC
ATAAAAGAGGTACAAAGGAGTTACGTCTTGACACAGGGTCCACCTCCTCACACACACACATGCTGCCACTTCTACTTCAT
GGTATTGGCAACAAAAGACCAAAGCCGCCAGTTGTGCTAAACCACATTGTGCAGAAAGACTCAGTAAACATGCACAGTAC
TGGCTAACAGACTGCTGAGAGTCACTGTTTAAAGAAACAGAATTCAGTGTGAAACTTTTGTCAGAAGATATGAAGTCATC
TTATATGGAACATCTACTACAATTAGAAAATACCGGTAGTGGTGAAACCAGAACAATAGCTCATTTCATTATACTACCTG
GCCAGATTTTGGAGTCCCAGAATCACCAGCTTCTTTTCTCAATTCCTTGTCTGAAGTGAAAGAATCTGGCGCCTTGAGCC
CGACCACTGTCCTGCAGTGATCCACTGTAGTGCAGGTATTGGGCACTTAGAAGCCTTCTTTCTGGTAGGTACCTAACTTG
TTCAGATGGAAAATGAAGGAGATATTAACATTAAGCAAGTGTTATTGAGTATGAGAAAATAATGAGTAGGACTTATTCAG
ACACCAGATCAACTTATATTCTCATACATGGCTATCATAGAAGGAGCAAGGTATATAAGGGGAGATTCTAGTATA

Alignment

ORF - retro_ogar_3429 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 73.06 %
• Parental protein coverage: 64.25 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 6

Retrocopy - Parental Gene Alignment:

Parental  RDVSPYDHSRVKLQNTENDYINASL-VDIEEAQRSYVLTQASGPLPNTCCHFWLMV-WQQKTKAV-VMLN
          R..SPYDHS..KLQNT.NDYINA...VDI.E.QRSYVLTQ...P...TCCHF..MV.WQQKTKA..V.LN
Retrocopy RN*SPYDHSHIKLQNTANDYINAPE<VDIKEVQRSYVLTQGPPPHTHTCCHFYFMV>WQQKTKAA>VVLN

Parental  RIVEKDSV-KCAQYWPTDDQEMLFKETGFSVKLLSEDVKSYYTVHLLQLENMSSGETRTISHF-HYTTWP
          .IV.KDSV.K.AQYW.TD..E.LFKET.FSVKLLSED.KS.Y..HLLQLEN..SGETRTI.HF.HYTTWP
Retrocopy HIVQKDSV<KHAQYWLTDC*ESLFKETEFSVKLLSEDMKSSYMEHLLQLENTGSGETRTIAHF<HYTTWP

Parental  DFGVPESPASFLNFLFKVRESGSLNP-DHGPAVIHCSAGIGRSGTFSLVDTCLVLMEKGEDINIKQVLLG
          DFGVPESPASFLN.L..V.ESG.L.P.DH.PAVIHCSAGIG....F.LV.T.LV.ME...DINIKQVLL.
Retrocopy DFGVPESPASFLNSLSEVKESGALSP<DHCPAVIHCSAGIGHLEAFFLVGT*LVQMENEGDINIKQVLLS

Parental  MRKYRMGLIQTPDQLRFSYMAIIEGAKYIKGDSNI
          MRK...GLIQTPDQL.FSYMAIIEGA.YI.GDS.I
Retrocopy MRK**VGLIQTPDQLIFSYMAIIEGARYIRGDSSI

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Otolemur garnettii was not studied using RNA-Seq expression data.

ChIP-Seq

Otolemur garnettii was not studied using ChIP-Seq data.

EST

Otolemur garnettii was not studied using EST data.

TSS

Otolemur garnettii was not studied using FANTOM5 data.

Lab

retro_ogar_3429 was not experimentally validated.

Homology

Retrocopy orthology:

Otolemur garnettii 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 14 parental genes, and 22 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	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,