RetrogeneDB ID: retro_etel_1009

Retrocopy location

• Organism: Lesser hedgehog tenrec (Echinops telfairi)
• Coordinates: scaffold_200016:10904..12364(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSETEG00000012122
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: DDX5
• Ensembl ID: ENSETEG00000019950
• Aliases: None
• Description: DEAD (Asp-Glu-Ala-Asp) box helicase 5 [Source:HGNC Symbol;Acc:2746]

Sequence

>retro_etel_1009
GGTTATTTGAATGACCAAGACCGTGGCTGGGATGGAGGGTTTGGGGCACCTCGATTTGGAGGAAGTAGGGGAGTGCCCCT
GTCTGGAAAGAAATTCGGAAATCTCGGGGAGAAACTAGTTAAAAAGAAGTGGAATCTCGACAAACTGCCCAAATTTGAGA
AGAAATTTTATCAAAAACATCCTGATTTGGCTGGGCGCACAGCGTAAAATGTGGAGACATAACAGAAGAAGCAAGGAAGT
TACAGTTAGAGGACACAACTGCCCGAAGCCAGTTTTGAATGTTTATGAAGCAAACTTCCCTGCAAATGTCATGGATGCGA
TTGCAAGACAGAACTTTACAGAACCTACCGCCATTCAAACTCAGAGGTGGCCAGTTGCTCTAAGTGGATTGGATATGGTT
GGAGTAGCACAGACTGCATCCGGGAAAACGTTCTTACTTGCTGCCTGCCATTGTCCACATCAATCATCAGCCATTCCTAG
AGAGAGGTGATGGGCCTATTTGCTTGGTGCTGGCGCCAACTCGAGAACTGGTCCAACAGGTACAGCAGGTAGCTGCTGAA
TACTGTAGAACATGCCGCTTGAAGTCTACTTGCATCTATGGTGGAGCTCCCAAGGGACTACAGCTATGTGATATGGAGAG
AGGTGTGGAAATCTGTATTCAACACCTGGAAAACGGATTGACTTTTTAGAGTGGGAAAACCAGTCTGAGAACAACTTACC
TTGTCCTTGATGAGGCTGATAGAATGCTTGATATGGGCTTGGAGCCCCAAATAAGGAAGATTGTGGACCAGCTCAGACCC
GACAGACAAGCCTTAATGTGGAGAGCAACTTGGCCAAAAGGAGTAAGACGGCTTGATGAAGATTCCCTGAAACATTCACA
TAAACATCGGTGCGTTGGAACCGAGAGCAACCAAACCATTCTTCAGTTTGTGGATGTGTGTCGTGAGAAGGATGAAAAAC
GGATTCGTCTAATGGAAGAGATAATGAGTGAGAAGGAGAATAAAACCATTGTTTTTGTTGAAACCAAAAGAAGATGCGGT
GAACTTACCAGAAAAATGAGGAGAGATGGGTGGCCTGCCATAGGTATCCATGGCCACAAGAGTCAACAGGAGTGAGGCTG
GGTTCTAAATGAATTCAAACATGGAAAAACTCCTATTCTGATTGCTATAGATGTGGCCTCCAGAGGGCTAGATCTGGAAG
ATGTGAAATTTGTCATCAATTATGACTACCCTAACTTAGAGGATTATATTCACCGAATTGGAAGAAACGATCGCAGTACC
AAAACGGGCACAGCATACACTTTCTTTACACCTAATAACATACAGCAAGTGAGCGACCTTATCTCTGTGCTTCAGGAAGC
CAATCAAGCAATTAATCCCAACTTGCTTCAGCTGGTTGAAGACAGAGGTTCAGGTCGTTCCAGGGGTAGAGGAGGCATGA
AGGATGACCGACGGGACAAG

Alignment

ORF - retro_etel_1009 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 83.83 %
• Parental protein coverage: 80.33 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 7

Retrocopy - Parental Gene Alignment:

Parental  GYSSDRDRGRDRGFGAPRFGGSRAGPLSGKKFGNPGEKLVKKKWNLDELPKFEKNFYQEHPDLTRRTAQD
          GY..D.DRG.D.GFGAPRFGGSR..PLSGKKFGN.GEKLVKKKWNLD.LPKFEK.FYQ.HPDL..RTA..
Retrocopy GYLNDQDRGWDGGFGAPRFGGSRGVPLSGKKFGNLGEKLVKKKWNLDKLPKFEKKFYQKHPDLAGRTA*N

Parental  VET-YRRSKEVTVRGHNCPKPVLNFYEANFPANVMDVIARQNFTEPTAIQAQGWPVALSGLDMVGVAQTG
          VET..RRSKEVTVRGHNCPKPVLN.YEANFPANVMD.IARQNFTEPTAIQ.Q.WPVALSGLDMVGVAQT.
Retrocopy VET>NRRSKEVTVRGHNCPKPVLNVYEANFPANVMDAIARQNFTEPTAIQTQRWPVALSGLDMVGVAQTA

Parental  S-GKTLSYLLPAIVHINHQPFLERGDGPICLVLAPTRELAQQVQQVAAEYCRACRLKSTCIYGGAPKGPQ
          S.GK..SYLLPAIVHINHQPFLERGDGPICLVLAPTREL.QQVQQVAAEYCR.CRLKSTCIYGGAPKG.Q
Retrocopy S>GKR-SYLLPAIVHINHQPFLERGDGPICLVLAPTRELVQQVQQVAAEYCRTCRLKSTCIYGGAPKGLQ

Parental  IRDLERGVEICI-ATPGRLIDFLE-CGK-TNLRRTTYLVLDEADRMLDMGFEPQIRKIVDQIRPDRQTLM
          ..D.ERGVEICI..TPG..IDFLE..GK.T.LR.TTYLVLDEADRMLDMG.EPQIRKIVDQ.RPDRQ.LM
Retrocopy LCDMERGVEICI<STPGKRIDFLE<VGK<TSLR-TTYLVLDEADRMLDMGLEPQIRKIVDQLRPDRQALM

Parental  WSATWPKEVRQLAEDFLKD-YIHINIGALE-LSANHNILQIVDVCHDVEKDEKLIRLMEEIMSEKENKTI
          W.ATWPK.VR.L.ED.LK...I.I..GALE....N..ILQ.VDVC...EKDEK.IRLMEEIMSEKENKTI
Retrocopy WRATWPKGVRRLDEDSLKH>HINI--GALE<TESNQTILQFVDVCR--EKDEKRIRLMEEIMSEKENKTI

Parental  VFVETKRRCDELTRKMRRDGWPAMGIHGDKSQQERDWVLNEFKHGKAPILIATDVASRGLDVEDVKFVIN
          VFVETKRRC.ELTRKMRRDGWPA.GIHG.KSQQE..WVLNEFKHGK.PILIA.DVASRGLD.EDVKFVIN
Retrocopy VFVETKRRCGELTRKMRRDGWPAIGIHGHKSQQE*GWVLNEFKHGKTPILIAIDVASRGLDLEDVKFVIN

Parental  YDYPNSSEDYIHRIGRTARSTKTGTAYTFFTPNNIKQVSDLISVLREANQAINPKLLQLVEDRGSGRSRG
          YDYPN..EDYIHRIGR..RSTKTGTAYTFFTPNNI.QVSDLISVL.EANQAINP.LLQLVEDRGSGRSRG
Retrocopy YDYPN-LEDYIHRIGRNDRSTKTGTAYTFFTPNNIQQVSDLISVLQEANQAINPNLLQLVEDRGSGRSRG

Parental  RGGMKDDRRDR
          RGGMKDDRRD.
Retrocopy RGGMKDDRRDK

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_1009 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 10 parental genes, and 16 retrocopies.

Species	Parental gene accession	Retrocopies number
Echinops telfairi	ENSETEG00000019950	1 retrocopy	retro_etel_1009 ,
Felis catus	ENSFCAG00000003512	1 retrocopy	retro_fcat_172,
Myotis lucifugus	ENSMLUG00000009496	4 retrocopies	retro_mluc_1136, retro_mluc_1499, retro_mluc_1845, retro_mluc_2208,
Monodelphis domestica	ENSMODG00000003743	4 retrocopies	retro_mdom_1519, retro_mdom_1520, retro_mdom_1955, retro_mdom_1956,
Mus musculus	ENSMUSG00000020719	1 retrocopy	retro_mmus_788,
Pteropus vampyrus	ENSPVAG00000001932	1 retrocopy	retro_pvam_1267,
Rattus norvegicus	ENSRNOG00000030680	1 retrocopy	retro_rnor_1277,
Tupaia belangeri	ENSTBEG00000009490	1 retrocopy	retro_tbel_4260,
Tarsius syrichta	ENSTSYG00000012149	1 retrocopy	retro_tsyr_1269,
Tursiops truncatus	ENSTTRG00000008793	1 retrocopy	retro_ttru_1662,