RetrogeneDB ID: retro_etel_1942

Retrocopy location

• Organism: Lesser hedgehog tenrec (Echinops telfairi)
• Coordinates: scaffold_318244:40798..42031(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PTPN2
• Ensembl ID: ENSETEG00000005577
• Aliases: None
• Description: protein tyrosine phosphatase, non-receptor type 2 [Source:HGNC Symbol;Acc:9650]

Sequence

>retro_etel_1942
ATGACCAGGACCATGGAGCGGGAGTTTGAGAAGCTGGATATGCAGAATTACTGGCAGCAGCTGTACTCGGAAATTCAAAA
GGAGTCTCCAGACTATCCGCACCGAGTGGCCAAGTTTCCGGAAAACAGAAATCGAAACAGATACAGAAATGTGAGCCCCT
ACGATCACAGTCGCGTGAAACTGCAAGATACTGAAAACGACTATATTAACGCCAGCTTTGTGGTCATGGAGGAGGCGCAC
AGGAGGTACATCTTAACGCAAGGCCCGCTCCCCAACACCCGCTCTCATTTCTGGCTCATGGTTTGGCAGCAAGGGACAGA
GGCCATTGTCATGTTAAGCCGGCTGGTGGAGCAAGGGAAGGAGAAATGTGTGAGGTACTGGCCCGCCAAGGGGGGGCCCC
AGATGCTGTTTCGGGAAACGGGGCTCAGCGTGGAGCTGCTAACCGAAGAGGTGAAACCCCACTACACAGAGCACCGCCTG
CGATTACGAAGCCTGGGCAGTGGGCAAAGCAGGGCCATCGCTCACTTTCACTACACCACCTGGCCCGACTTCGGTGTCCC
AGAGTCCCCAGCTTCCCTGCTCCACTTCCTGTCCCAAGTGAGAGTCTCTGGCTCCCTGAAGGGGGAGCACGGGCCCCCCG
TGGTGCACTGCAGCGCTGGCGTGGGCCGCTCGGGCACATTCTCCTTCATAGACATCTGCCTTATTCTGATGGCACAGGGA
CATGATATAACGATCAAACAAGTGCTACTGAAGATGAGAAAGTATCGAAGGGGCCTGATTCAGACCCCAGAACAACTACG
ATTCTCATACAGGGCTATCATCGAAGGAGCCCAGTTTACCAAGGGGGACTGGAATACAGAGAAACGATGGAGAGAACTTT
CTAAGGAAAACGTGTCCCCTGCTTTTGATCGTTCACCCACCATGATAAAGACCGAGACATATAATAGTAACAAAACAGGC
TTGGAAGAAGGAAAGGGTACAAGACTGTCCTCTGAGAGCCAAGCTCCTGGAAAGGAAAGGAGGGAGAGGGTTCTGCGAGA
ACGAGTGCTAGAGGACAGACAAGCGAACACAGCTCAGAGAGTGCCGCGGATGGAACAGAGGCTAAAAGAGACCCAACAAA
TGAGAAAAACGCAGTTATATTGGCAACATGTCTTCACTAAGATCGGGGTTGGGTCCGTCCTTGTGGTTGGCATTTTGGTT
GGCTGGACACTATTTTTTCAGCAAAATGCCTTA

Alignment

ORF - retro_etel_1942 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 68.51 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MSVTLEREFEEMDTQNCWXXXXXEIRNESHDYPHRVAKFPENRNRNRYRDVSPYDHSRVTLQSTENDYIN
          M..T.EREFE..D.QN.W.....EI..ES.DYPHRVAKFPENRNRNRYR.VSPYDHSRV.LQ.TENDYIN
Retrocopy MTRTMEREFEKLDMQNYWQQLYSEIQKESPDYPHRVAKFPENRNRNRYRNVSPYDHSRVKLQDTENDYIN

Parental  ASLVDIEEAQRSYILTQGPLPNTCCHFWLMVWQQKTKAIVMLNRVVEKESVKCAQYWPTKDDREVLFKET
          AS.V..EEA.R.YILTQGPLPNT..HFWLMVWQQ.T.AIVML.R.VE....KC..YWP.K.....LF.ET
Retrocopy ASFVVMEEAHRRYILTQGPLPNTRSHFWLMVWQQGTEAIVMLSRLVEQGKEKCVRYWPAKGGPQMLFRET

Parental  GFSVKLLTEDVKSYYTVHLLQLENINSGETRTISHFHYTTWPDFGVPESPASFLNFLFKVRESGSLKAEH
          G.SV.LLTE.VK..YT.H.L.L....SG..R.I.HFHYTTWPDFGVPESPAS.L.FL..VR.SGSLK.EH
Retrocopy GLSVELLTEEVKPHYTEHRLRLRSLGSGQSRAIAHFHYTTWPDFGVPESPASLLHFLSQVRVSGSLKGEH

Parental  GPVVVHCSAGIGRSGTFSLVDTCLILLEKGNDINIKQVLLNMRKFRMGLIQTPDQLRFSYMAMIEGAKFI
          GP.VVHCSAG.GRSGTFS..D.CLIL...G.DI.IKQVLL.MRK.R.GLIQTP.QLRFSY.A.IEGA.F.
Retrocopy GPPVVHCSAGVGRSGTFSFIDICLILMAQGHDITIKQVLLKMRKYRRGLIQTPEQLRFSYRAIIEGAQFT

Parental  KGD-NIQKRWKELSKEDLSPAFDHSPTKIMTEKYNGNRIALEEGKLAGDRCSGLSSKIQETVEERSESVL
          KGD.N..KRW.ELSKE..SPAFD.SPT.I.TE.YN.N...LEEGK..G.R.S...S..Q....ER.E.VL
Retrocopy KGDWNTEKRWRELSKENVSPAFDRSPTMIKTETYNSNKTGLEEGK--GTRLS---SESQAPGKERRERVL

Parental  RKRVREDRKANTAQKVQQMKQRLNETERKRKRWLYWQPIFTKIGFVSVLLVGAFVGWTLFFQQNAL
          R.RV.EDR.ANTAQ.V..M.QRL.ET...RK..LYWQ..FTKIG..SVL.VG..VGWTLFFQQNAL
Retrocopy RERVLEDRQANTAQRVPRMEQRLKETQQMRKTQLYWQHVFTKIGVGSVLVVGILVGWTLFFQQNAL

Legend:

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

Expression

RNA-Seq

Echinops telfairi was not studied using RNA-Seq expression data.

ChIP-Seq

Echinops telfairi was not studied using ChIP-Seq data.

EST

Echinops telfairi was not studied using EST data.

TSS

Echinops telfairi was not studied using FANTOM5 data.

Lab

retro_etel_1942 was not experimentally validated.

Homology

Retrocopy orthology:

Echinops telfairi 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,