RetrogeneDB ID: retro_itri_484

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393294.1:16994828..16995408(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RABGGTB
• Ensembl ID: ENSSTOG00000021824
• Aliases: None
• Description: Rab geranylgeranyltransferase, beta subunit [Source:HGNC Symbol;Acc:9796]

Sequence

>retro_itri_484
GGGAGAAATGATACAAGATTCTCCTTTTGTGCAGTGACAACTTTGGCTCTGTTGGGGAAACTTGATGCTATTAATGTGGA
AAAGGCAATCGAATTTGTTTTATCCTGTATGAACTTTGATGGTGGATTGGGTTGTAAACCTGGTTCTGAATCCCATGCTG
AACAGATCTATTGTTGCACAGGACTCCTGGCTATTACTAGTCATTTGCATCAAATAAGTTCTGATTTACTTGGTTGGTAG
CTTTGTGAACTGACAGTTACCTTCAGGAGGACTCAATGGAAGGCTGGAGAAGTTACCAGATGTGTGCTATTTGTGGTGGG
TATTGGCTTCCCTAAAGATAATTAGAAGGCTTCAGTGGATTGACAGAAACAAACTGCAAGATTTCATTTTGGCATGTCAA
GATGAAGAAGCTGGAGGGTTTGCAGATAGGCCAGGAGACATGGTGGATCCTTTTTCTTATATTATTTGGCATTGCTGGAT
TGTCACTTTTGGGGGAAGAATAGACTAAACCTGTTAGTCCTGTTTTTTGCATGACTGAAGAAGTGCTTCAAGAGTCAATG
TTCAGCCTGAACTAGTGAGC

Alignment

ORF - retro_itri_484 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.2 %
• Parental protein coverage: 58.31 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  GEIDTRFSFCAVATLALLGKLDAINVEKAIEFVLSCMNFDGGFGCRPGSESHAGQIYCCTGFLAITSQLH
          G..DTRFSFCAV.TLALLGKLDAINVEKAIEFVLSCMNFDGG.GC.PGSESHA.QIYCCTG.LAITS.LH
Retrocopy GRNDTRFSFCAVTTLALLGKLDAINVEKAIEFVLSCMNFDGGLGCKPGSESHAEQIYCCTGLLAITSHLH

Parental  QVNSDLLGWWLCER-QLPSGGLNGRPEKLPDVCYSWWVLASLKIIGRLHWIDREKLRAFILACQDEETGG
          Q..SDLLGW.LCE..QLPSGGLNGR.EKLPDVCY.WWVLASLKII.RL.WIDR.KL..FILACQDEE.GG
Retrocopy QISSDLLGW*LCEL>QLPSGGLNGRLEKLPDVCYLWWVLASLKIIRRLQWIDRNKLQDFILACQDEEAGG

Parental  FADRPGDMVDPFH-TLFGIAGLSLLGEEQIKPVSPVFCMPEEVLR-RVNVQPELVS
          FADRPGDMVDPF...LFGIAGLSLLGEE..KPVSPVFCM.EEVL..RVNVQPELVS
Retrocopy FADRPGDMVDPFS>ILFGIAGLSLLGEE*TKPVSPVFCMTEEVLQ<RVNVQPELVS

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_484 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_484 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 8 parental genes, and 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000011052	1 retrocopy	retro_acar_155,
Canis familiaris	ENSCAFG00000020392	1 retrocopy	retro_cfam_2104,
Choloepus hoffmanni	ENSCHOG00000009456	2 retrocopies	retro_chof_1851, retro_chof_260,
Mus musculus	ENSMUSG00000038975	1 retrocopy	retro_mmus_1030,
Otolemur garnettii	ENSOGAG00000007665	1 retrocopy	retro_ogar_1089,
Sorex araneus	ENSSARG00000007392	1 retrocopy	retro_sara_207,
Ictidomys tridecemlineatus	ENSSTOG00000021824	1 retrocopy	retro_itri_484 ,
Tursiops truncatus	ENSTTRG00000014126	3 retrocopies	retro_ttru_1391, retro_ttru_1767, retro_ttru_214,