RetrogeneDB ID: retro_itri_522

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393298.1:15210271..15210723(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RMDN1
• Ensembl ID: ENSSTOG00000005267
• Aliases: None
• Description: regulator of microtubule dynamics 1 [Source:HGNC Symbol;Acc:24285]

Sequence

>retro_itri_522
AAAAGTGAGTCAAGTTTTGCTGCAATCTGCATTAGAAAGATTTAGCTGCATAATGTTGCTGATTATGAAGCCATCAATAT
TAAAATTTGCAAATGCCTACACTAACTAGGAGCATATTGAGAAACAAATTAAACTGAACCCTAAAGATTCTACCTCCATT
CGCCTTAAGAGTACAGGGTGCTACACATTTGTTCAAATGTCTTGGTACCAAAAAATAATTACTAAAATTGCTGTTTGCAA
CTCCTTCAAGCTCCATCTAGAAGGAGGACTTGACCAACTTTCATGGAGAAAAACAAATGGATCCAATCTTCCAGAGAAAA
AACTTGGCTTCTTTCAGGAAAGACATACATGAAGTTAAACAATAAAAACTTGCTGCTTTCTGGCTGATGAAAGCTAAGGC
CTTCCCAGCACACACAAAGGAGATGCAGACAGAAGCTGCTCAGTTGCTTTCA

Alignment

ORF - retro_itri_522 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 59.24 %
• Parental protein coverage: 66.23 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  KNESSFAAHKWYAICISDVGDYEGIKVKI-ANAYIIKEHFEKAIELNPKDATSVHLMGIWCYTFAEMPWY
          K.ESSFAA.....I....V.DYE.I..KI.ANAY...EH.EK.I.LNPKD.TS..L....CYTF..M.WY
Retrocopy KSESSFAAICIRKI*LHNVADYEAINIKI>ANAYTN*EHIEKQIKLNPKDSTSIRLKSTGCYTFVQMSWY

Parental  QRRIAK-MLFATPPSSTYEEALGYFHRAEQVDPNFYSKNL-LLLGKTYLKLKNK-KLAAFWLMKAKDYPA
          Q..I.K..LFATP.SS...E.L..FH...Q.DP.F..KNL.LL.GKTY.KL.NK.KLAAFWLMKAK..PA
Retrocopy QKIITK>LLFATPSSSI*KEDLTNFHGEKQMDPIFQRKNL>LLSGKTYMKLNNK<KLAAFWLMKAKAFPA

Parental  HTEEDKQVQTEATQLLT
          HT...K..QTEA.QLL.
Retrocopy HT---KEMQTEAAQLLS

Legend:

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

Expression

RNA-Seq

Ictidomys tridecemlineatus was not studied using RNA-Seq expression data.

ChIP-Seq

Ictidomys tridecemlineatus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_itri_522 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_522 was not experimentally validated.

Homology

Retrocopy orthology:

Ictidomys tridecemlineatus 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 2 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Ictidomys tridecemlineatus	ENSSTOG00000005267	2 retrocopies	retro_itri_522 , retro_itri_525,
Tursiops truncatus	ENSTTRG00000002271	1 retrocopy	retro_ttru_1444,