RetrogeneDB ID: retro_itri_525

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393298.1:964018..964445(-)
• Located in intron of: ENSSTOG00000010105

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_525
TATGCAATCTGCATTAGTGATGTTGGAGATTACGAAGTCATCAAGATTAAAACTGCAAATGCCTACATTTCAAGGAACAT
TATGAGAAAGCAATTGAAATGAAACCTGAAGATGCTATCTCAATTTACCTGATAAGTATTTGGAGCTATGCATTTGCTGA
AATTCCTTGGTATCAAAGAACTGCTAAAATGCTGTTTGTACCTCCTCCTAGTTTCATCTATGAGGAGGCCTTGGGCTACT
TTCACAGGGAGAACAGGTGGATTCAAACTTCTGCAGCAAAAACTTGCTTCTTTTAGGAAAGACATTCTTGAAGTTAAAAA
ACAAAAAGCTGGCTGCTTTCTGGTTAATGAAAGCCAAGGACTATTCAGTACACATGGAGGAAGATAAACAAATACAGAGA
GAAGCTGCTCAGTTGCTTACAGGTTTG

Alignment

ORF - retro_itri_525 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 76.03 %
• Parental protein coverage: 62.34 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  YAICISDVGDYEGIKVKIANAYI-IKEHFEKAIELNPKDATSVHLMGIWCYTFAEMPWYQRRIAKMLFAT
          YAICISDVGDYE.IK.K.ANAYI..KEH.EKAIE..P.DA.S..L..IW.Y.FAE.PWYQR..AKMLF..
Retrocopy YAICISDVGDYEVIKIKTANAYI<FKEHYEKAIEMKPEDAISIYLISIWSYAFAEIPWYQRT-AKMLFVP

Parental  PPSSTYEEALGYFHR-AEQVDPNFYSKNLLLLGKTYLKLKNKKLAAFWLMKAKDYPAHTEEDKQVQTEAT
          PPS..YEEALGYFHR..EQVD.NF.SKNLLLLGKT.LKLKNKKLAAFWLMKAKDY..H.EEDKQ.Q.EA.
Retrocopy PPSFIYEEALGYFHR<GEQVDSNFCSKNLLLLGKTFLKLKNKKLAAFWLMKAKDYSVHMEEDKQIQREAA

Parental  QLLTDL
          QLLT.L
Retrocopy QLLTGL

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_525 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_525 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.

---

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,