RetrogeneDB ID: retro_shar_293

Retrocopy location

• Organism: Tasmanian devil (Sarcophilus harrisii)
• Coordinates: GL841247.1:1127828..1128442(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CINP
• Ensembl ID: ENSSHAG00000007660
• Aliases: None
• Description: cyclin-dependent kinase 2 interacting protein [Source:HGNC Symbol;Acc:23789]

Sequence

>retro_shar_293
ATGAAGAACTCTGGCATGGATACTCCCAAAAGAACTGTCTTATCAGTCAGCACAAGAAAAATTAAGGACAATGCTGCATA
TTGACATAATTTATCAAAATGAGATTCTTTCAATAGATTGGAGTTTTCTGTTGCAAACAAAATACCAACATCAAAATTAG
TGCACTTACTAAAGACAAGGTAGAACCAAAATACAGTAGCATTACTTCTGGCTTTCATTCTCAAAAGATATACCCAAAAT
ATAATGAGGAATTTGAGATGTTATGCAACGAACTTCAAAACACTTTGGAAAATTTGGCTAAGGAACAAGTGCAAATGGAA
AAGTTAGCATCAACCACTAAAAGAATTTATAATCTAGAAAATTACTACCTAGGAAAGGGAAACCAATTTTCCATACATGG
TCCACAACCTACTTCTATGAAATTTCTCCATAAGTTTTCAGAAATGTACAAGAAAGAAATATTCCTCAAACACATCATTG
TTGAAGAGCTCACCCATGCTATGAACCAGGATCTCATTTTAAGCTACTTCTCTATGTAGTTGTACCAGTTTTATGTTCAG
AACAGCAGGCTTGATGTGGAAAGCATGCTCCTTAAAAATAGACATTGAGCATTA

Alignment

ORF - retro_shar_293 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 66.99 %
• Parental protein coverage: 97.65 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  VKNSGIITPKRTVLSVSARKIKDNAADWHNLLLKWETLNNVGFSIANKIG-NIKISALTEDKVELECNSI
          .KNSG..TPKRTVLSVS.RKIKDNAA..HNL..K....N...FS.ANKI..NIKISALT.DKVE....SI
Retrocopy MKNSGMDTPKRTVLSVSTRKIKDNAAY*HNLS-K*DSFNRLEFSVANKIP<NIKISALTKDKVEPKYSSI

Parental  ASGICSQKAHPKYNEELEMLCKELHDTLANLAKVQMKMEKLTSTTKGICNLENYHRGNGNQTPLFHTWPT
          .SG..SQK..PKYNEE.EMLC.EL..TL.NLAK.Q..MEKL.STTK.I.NLENY..G.GNQ.......PT
Retrocopy TSGFHSQKIYPKYNEEFEMLCNELQNTLENLAKEQVQMEKLASTTKRIYNLENYYLGKGNQFSIHGPQPT

Parental  TYFYEVSHKLSEMYKKEILLKRIIVEELAHATNQDLILSYLSMWLYQPYVENSRLDVESMLLETGHRAL
          .......HK.SEMYKKEI.LK.IIVEEL.HA.NQDLILSY.SM.LYQ.YV.NSRLDVESMLL...H.AL
Retrocopy S--MKFLHKFSEMYKKEIFLKHIIVEELTHAMNQDLILSYFSM*LYQFYVQNSRLDVESMLLKNRH*AL

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_293 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 4 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Monodelphis domestica	ENSMODG00000013323	1 retrocopy	retro_mdom_1091,
Oryctolagus cuniculus	ENSOCUG00000026866	1 retrocopy	retro_ocun_1274,
Otolemur garnettii	ENSOGAG00000009451	1 retrocopy	retro_ogar_321,
Sarcophilus harrisii	ENSSHAG00000007660	3 retrocopies	retro_shar_293 , retro_shar_294, retro_shar_594,