RetrogeneDB ID: retro_itri_1873

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH394305.1:53665..54460(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: TRAF4
• Ensembl ID: ENSSTOG00000005085
• Aliases: None
• Description: TNF receptor-associated factor 4 [Source:HGNC Symbol;Acc:12034]

Sequence

>retro_itri_1873
ATGCCCGGTTTCCACTACAAGTTCCTAGAAAAGCCCAAGCAATGGCTGTTGTTCCTGCTATGCAGGAAACCCATGCACAA
GCCTGTGCAGGATTCTACCCTTGGCCAATGCTTCTGCAACACCTGCCTGCAGGAGTTCCTTAGTGAAAGAGTCTGCAAAT
GCCCTGAGGACCAAGTTCCCTTGGACTATGCCAAGATTTACCCAGACCCAGAGCTGGAGGTCCATGTGCTAGGCCTGTTC
ATCCGCTGAATCCACAGTGAGGAGGACTGCTGCTGGAGTGGGCCACGTCGTCATTTACAAAGAAACCTGAATACCTGCAG
CTTCAATGTAATTCCCTGGCCCAATCGCTGTCCTGCCAAGCTGAATCGCCATGATCTGCCTGCACACTTGCAACGTGATT
GCCCTAAGCGGCGCCACAAGTGCTAGTTCTGTGGCTGTGACTTCAGTGAGGAAGCCTATGAGAACTATGAGGGTATGTTC
CCCCAAGAGAGTGTGTACTGTGAGGAAAAGCATAGTGCCTGCATGATGTGGTGACTACTGGCCCAGCAGGCCACTTCTGA
GTGGCCCAAGCGCACCCAGCCTTGTACCTATTGCACAAAGGAATTTATCTTTGACACCATCCAGAGTCACCAGTACCAGT
GCCCCAGGTTGCCTGTGCCCTGCCCTAACCAGTGTGGTGGCATGGGCACTGTGGCTTGGGAGGCTTTTCCAAATTATCTG
ACGGACAGAGGTAGTATTGCCTTGGTGCTATGTCTGTTCAAAGACTCCAGTTGCAAGCACAGGGTAAGATGCCCC

Alignment

ORF - retro_itri_1873 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 78.11 %
• Parental protein coverage: 55.74 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MPGFDYKFLEKPKRRLLCPLCGKPMREPVQVSTCGHRFCDTCLQEFLSEGVFKCPEDQLPLDYAKIYPDP
          MPGF.YKFLEKPK..LL..LC.KPM..PVQ.ST.G..FC.TCLQEFLSE.V.KCPEDQ.PLDYAKIYPDP
Retrocopy MPGFHYKFLEKPKQWLLFLLCRKPMHKPVQDSTLGQCFCNTCLQEFLSERVCKCPEDQVPLDYAKIYPDP

Parental  ELEVQVLGLPIRCIHSEEGCRWSGPLRHLQGHLNTCSFNVVPCPNRCPAKLSRRDLPAHLQHDCPKRRLK
          ELEV.VLGL.IR.IHSEE.C.WSGP.RHLQ..LNTCSFNV.P.PNRCPAKL.R.DLPAHLQ.DCPKRR.K
Retrocopy ELEVHVLGLFIR*IHSEEDCCWSGPRRHLQRNLNTCSFNVIPWPNRCPAKLNRHDLPAHLQRDCPKRRHK

Parental  CEFCGCDFSGEAYESHEGMCPQESVYCENKCGARMMRRLLAQHATSECPKRTQPCTYCTKEFVFDTIQSH
          C.FCGCDFS.EAYE..EGM.PQESVYCE.K..A.MM..LLAQ.ATSE.PKRTQPCTYCTKEF.FDTIQSH
Retrocopy C*FCGCDFSEEAYENYEGMFPQESVYCEEKHSACMMW*LLAQQATSEWPKRTQPCTYCTKEFIFDTIQSH

Parental  QYQCPRLPVPCPNQCG-VGTVAREDLPNHLKDSCSTALVLCPFKDSGCKH--RCP
          QYQCPRLPVPCPNQCG..GTVA.E..PN.L.D..S.ALVLC.FKDS.CKH..RCP
Retrocopy QYQCPRLPVPCPNQCGGMGTVAWEAFPNYLTDRGSIALVLCLFKDSSCKHRVRCP

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_1873 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_1873 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 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Macropus eugenii	ENSMEUG00000003314	1 retrocopy	retro_meug_1907,
Ictidomys tridecemlineatus	ENSSTOG00000005085	1 retrocopy	retro_itri_1873 ,