RetrogeneDB ID: retro_itri_1354

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393450.1:2973505..2973929(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: HTATIP2
• Ensembl ID: ENSSTOG00000011216
• Aliases: None
• Description: HIV-1 Tat interactive protein 2, 30kDa [Source:HGNC Symbol;Acc:16637]

Sequence

>retro_itri_1354
AATATGCATCAAGAAGTGGTGGACTTTGAAAAACTGGAAGACTAAGGTGTCTTACAAAGTCATGATGTTGGAATCTGTTG
CCTGAATACCACCAGAAACAAAGCTGGGATGGAGGGATTTGTTTGTGTTGACTGAAATCTCATGCTGGAGACTGCAGAGC
TGGAAAAAGCTGAATGGTGCAAATATTTCAACTTGCTGTCCTCTAAAGGAACTGATAAGTCGAGCAATTTTTTATATTTA
CAAGTTAATTGAGAAGTAGAAGCCAGGGTTGGGGAATTAAAATTTGATCTCCACTCAGTATTTAGGCCTGGAGTTTTGTC
ATGTGGTAGGTAAGAATCTCACCCAGGTGAATGGTTAGAAATTCTTAGGCTCCTCACTAAAGTCTGGAGCCAGTGGACAC
TCGGTGTCTGTGGTGACTGTGGCT

Alignment

ORF - retro_itri_1354 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 66.9 %
• Parental protein coverage: 60.5 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  NVNQEVVDFEKLEDYASAFQGHDVGFCCLGTTRSKAGAEGFVRVDRDYVLKSAELAKSGGCKHFNLLSSK
          N..QEVVDFEKLED.....Q.HDVG.CCL.TTR.KAG.EGFV.VD....L..AEL.K...CK.FNLLSSK
Retrocopy NMHQEVVDFEKLED*G-VLQSHDVGICCLNTTRNKAGMEGFVCVD*NLMLETAELEKAEWCKYFNLLSSK

Parental  GADKSSNFLYLQVKGEVEARVGELKFDRYSIFRPGVLLCNRQESRPGEWLIRKFFGFLPDSW-ASGHSVP
          G.DKSSNFLYLQV..EVEARVGELKFD..S.FRPGVL.C.R.ES.PGEWL.......L...W.ASGHSV.
Retrocopy GTDKSSNFLYLQVN*EVEARVGELKFDLHSVFRPGVLSCGR*ESHPGEWL--EILRLLTKVW>ASGHSVS

Parental  VLTLA
          V.T.A
Retrocopy VVTVA

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_1354 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_1354 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 5 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000006718	1 retrocopy	retro_cjac_967,
Loxodonta africana	ENSLAFG00000018703	1 retrocopy	retro_lafr_244,
Oryctolagus cuniculus	ENSOCUG00000000749	1 retrocopy	retro_ocun_822,
Pongo abelii	ENSPPYG00000003421	1 retrocopy	retro_pabe_1288,
Ictidomys tridecemlineatus	ENSSTOG00000011216	2 retrocopies	retro_itri_1354 , retro_itri_1523,