RetrogeneDB ID: retro_itri_975

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393353.1:8421168..8422074(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: C1orf27
• Ensembl ID: ENSSTOG00000023665
• Aliases: None
• Description: chromosome 1 open reading frame 27 [Source:HGNC Symbol;Acc:24299]

Sequence

>retro_itri_975
CATGATATCCATGACCCAAAGAGTTCAGCAAGACCAGCCAATTGGAAGTATCAAAGTGGACTGTCTACTTCATGGCTTTC
TCTAGATTGTACCATTCACATTGATATTCACATTCCACTTTCTTCTACTTCTGTCAGCTAGACTCTGGAAACAAATACAA
AGAATGGACTTCCACACTGGGCCAAGCAAATAGAAAATGATGTTTATTTGATTAATGGACAAGTTAAAAATGAAGATTGT
GATCTATTAGAAGGACAGAAAAAATCTTTCAGAGGAAATACTCAAGCAACTAGTCATTCTTTTGATGTGAGCGTGCTAAC
ACAATTGCTTCTGAATTCAGACCACAGATCTACAGCCACAGTTCCGATCTGCAGTGGTTCTGTAAACCTTAAGGGTTCTG
TGAAATGCAGAGCTTATATTCACAGCAACAAACCCAAGGTTAAAGACGCTATGCAGGCAGTGAAGAGAGAGATATTGAAC
ACAGTTGCTGATGGTTGTGAAATACTATTTGAGGACCTGCTTTTGAATGAAATCCCAGAAAAAAAAGATTCTGAAAAAGA
GTTCTACATTCTCCCTCACCGAGTTTTTGTCCCCATTCCTGGATCCACTGTAAAGTTATGTGATTATAAATTTGGTGATG
AATCAGCCGAAGAAATCAGAGACCATTTTATAGAGATGTTAGATCATATGGTTCAAATAGAAGATTTGGAAATTGCAGAG
GAAGTCAACACAGCTTGTATGAGCTCTATGAATAATGAAGCTTCATTGGAACACAAAGATGATAAACAACTAGAGCAACC
AATTGAAACTACAGTAATGTTGAAAATTCGGCAAAACATAGGTGTGATTGCAGCATTTGCAGTTGCAGTTCTTGCTGCGG
GTATCTCTTTTCATTACTTCAGTGAT

Alignment

ORF - retro_itri_975 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 94.04 %
• Parental protein coverage: 66.67 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  YDVHDPKSSARPADWKYQSGLSTSWLSLDCTIHIDIHIPLSSTSVSYTLEKNTKNGLTRWAKQIENGVYL
          .D.HDPKSSARPA.WKYQSGLSTSWLSLDCTIHIDIHIPLSSTSVS.TLE.NTKNGL..WAKQIEN.VYL
Retrocopy HDIHDPKSSARPANWKYQSGLSTSWLSLDCTIHIDIHIPLSSTSVS*TLETNTKNGLPHWAKQIENDVYL

Parental  INGQVKDEDCDLLEGQKKSFRGNTQATSHSFDVRVLTQLLLNSDHRSTATVQICSGSVNLKGSVKCRAYI
          INGQVK.EDCDLLEGQKKSFRGNTQATSHSFDV.VLTQLLLNSDHRSTATV.ICSGSVNLKGSVKCRAYI
Retrocopy INGQVKNEDCDLLEGQKKSFRGNTQATSHSFDVSVLTQLLLNSDHRSTATVPICSGSVNLKGSVKCRAYI

Parental  HSNKPKVKDAMQAVKRDILNTVADRCEILFEDLLLNEIPEKKDSEKEFYILPHRVFVPIPGSTIKLCDYK
          HSNKPKVKDAMQAVKR.ILNTVAD.CEILFEDLLLNEIP...DSEKEFYILPHRVFVPIPGST.KLCDYK
Retrocopy HSNKPKVKDAMQAVKREILNTVADGCEILFEDLLLNEIPXXXDSEKEFYILPHRVFVPIPGSTVKLCDYK

Parental  FGDESAEEIRDHFIEMLDHMVQIEDLEIAEEVNTACMSSMNNEASLEHKDDKQLEQPIKTTVMLKIRQNI
          FGDESAEEIRDHFIEMLDHMVQIEDLEIAEEVNTACMSSMNNEASLEHKDDKQLEQPI.TTVMLKIRQNI
Retrocopy FGDESAEEIRDHFIEMLDHMVQIEDLEIAEEVNTACMSSMNNEASLEHKDDKQLEQPIETTVMLKIRQNI

Parental  GVIAAFAVAVLAAGISFHYFSD
          GVIAAFAVAVLAAGISFHYFSD
Retrocopy GVIAAFAVAVLAAGISFHYFSD

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_975 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_975 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	ENSSTOG00000023665	1 retrocopy	retro_itri_975 ,
Tarsius syrichta	ENSTSYG00000011439	2 retrocopies	retro_tsyr_1023, retro_tsyr_217,