RetrogeneDB ID: retro_shar_502

Retrocopy location

• Organism: Tasmanian devil (Sarcophilus harrisii)
• Coordinates: GL849709.1:778572..779196(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CDKN3
• Ensembl ID: ENSSHAG00000008977
• Aliases: None
• Description: cyclin-dependent kinase inhibitor 3 [Source:HGNC Symbol;Acc:1791]

Sequence

>retro_shar_502
ATGAAGGTGTCCAATACATGAGGACAAATGAGTCTGACTAATCAAATGAAAGACCAATTGAAAATTAATAGACTCCATTT
TAGGTATAATAGCTACCCTTATCCATTGTAAATTGTTCTCAGTTTCTAAATTTATGTTTTCTTCTCGGTTGTAAATTTAA
AGATGTTAGATGAAATCTCCAAAAAGAACTTGAGAAAAAGTAAAGAATAGTATATAAGATATATTTCTGTTCCATACCAG
AAGAGAGCTATCAAAATACTGAATACCAAATCTTTTAGACTTCTATCAGTAGCATGGAATCATCTTTTGCTGTCATCCCA
TCCCAGATGGAGATATCTCTGATATAGACCCAATGTTGTAGAATACAAAGGAGCTTGTAGATTGTCTTTAAAATATCCAG
AAAACTTTAATTTATTGTTATGCAGGATTTGGACAATCTTGTCTTGTAATGGCTTGCTTCCTACTCTACGTATAGACACC
CCACAAGGGAATTGGCAGTCTTCAAGATATAAAAAGATCTGGGATCATACGGGCCATAAAGGAATATAACTATCTCTATG
ATTTCCAAGATGAACTGGCTGCACATCTATCAGAAAAGACTCAGTATTAAGATCTGTATCTAAA

Alignment

ORF - retro_shar_502 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 60.83 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 12
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  MKVPST-MQTSEFDSSDEEPVENEQTPFQVSWLPLSLVNCSQFLGLCSLPGCKFKDVRRNLQKDVE-ELK
          MKV..T.M.T.E.D.S.E.P.EN..TPF.V..LPLS.VNCSQFL.LC.L.GCKFKDVR.NLQK..E.E..
Retrocopy MKVSNT<MRTNESD*SNERPIEN**TPF*V**LPLSIVNCSQFLNLCFLLGCKFKDVR*NLQKELE<EKV

Parental  NYGIQDIFVFCTRGELSKYRVPNLLDFYQQHGIIIHHHPIPDGDTPDID-RCCGI-LQELAVCLENNRKT
          ...I.DIF.F.TR.ELSKY..PNLLDFYQ.HGII...HPIPDGD..DID..CC.I...EL..CL.N..KT
Retrocopy KNSI*DIFLFHTRRELSKY*IPNLLDFYQ*HGIIFCCHPIPDGDISDID>QCCRI<TKELVDCL*NIQKT

Parental  LIHCYGGLGRSCLVAACLLLYLSDTVSPQQAIDSLRDLRGSGAIQTIKQYNYLHDFRDKLAAHLS-TRDS
          LI.CY.G.G.SCLV.AC....L.....P...I.SL.D...SG.I..IK.YNYL.DF.D.LAAHLS...DS
Retrocopy LIYCYAGFGQSCLVMAC---FLLYV*TPHKGIGSLQDIKRSGIIRAIKEYNYLYDFQDELAAHLS<RKDS

Parental  VSRSVSR
          V.RSVS.
Retrocopy VLRSVSK

Legend:

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

Expression

RNA-Seq

Sarcophilus harrisii was not studied using RNA-Seq expression data.

ChIP-Seq

Sarcophilus harrisii was not studied using ChIP-Seq data.

EST

Sarcophilus harrisii was not studied using EST data.

TSS

Sarcophilus harrisii was not studied using FANTOM5 data.

Lab

retro_shar_502 was not experimentally validated.

Homology

Retrocopy orthology:

Sarcophilus harrisii 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 8 parental genes, and 12 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000012823	1 retrocopy	retro_chof_1806,
Echinops telfairi	ENSETEG00000018617	1 retrocopy	retro_etel_1763,
Felis catus	ENSFCAG00000015089	2 retrocopies	retro_fcat_135, retro_fcat_626,
Loxodonta africana	ENSLAFG00000014833	1 retrocopy	retro_lafr_637,
Macropus eugenii	ENSMEUG00000002497	3 retrocopies	retro_meug_1255, retro_meug_1768, retro_meug_1849,
Procavia capensis	ENSPCAG00000015559	1 retrocopy	retro_pcap_104,
Sarcophilus harrisii	ENSSHAG00000008977	1 retrocopy	retro_shar_502 ,
Tupaia belangeri	ENSTBEG00000010203	2 retrocopies	retro_tbel_1809, retro_tbel_4700,