RetrogeneDB ID: retro_itri_1756

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393724.1:33295..34112(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: TIPRL
• Ensembl ID: ENSSTOG00000014921
• Aliases: None
• Description: TIP41, TOR signaling pathway regulator-like (S. cerevisiae) [Source:HGNC Symbol;Acc:30231]

Sequence

>retro_itri_1756
ATGATAATCCACGGCTTCCAGAGCAGCCACCAGGACTTCTCCTTCCGCCCTGGAAGCTGACGGCCTCCAAGACCCGCATC
ATGAAGTCAGCGGATGTGGAGAGGTTAGCAGATGAATTGCACATGCCTTCTCTCCCTGAAATGATGTTTGGAGACAATGT
CATAAGAATCCAGCATGGCTCTGGCTTTGGGATCGAGTTCAATGCTACAGATGCATTAAGATGTGTAAACAACTACGAAG
GGGAATGCTTAAAGTGGCCTGTGGCGAAGAGTGGCAGGAAAGCAGGACGGAGGGCGAACACTCCAAAGAGGTTATTAAGC
CCTATGATTGAACCTATAAGACAGATTATAAAAAAACGTTACTTGGAGAATCTCTTAAATTAAAGGTTGTACCTACAACA
GATCATATAGATACAGAGAAATTGAAAGCCAGAGAACAGATTAAATTTTTTGAAGAAGTTCTCCTGTTTGAGGATGAACT
TCATGATCATGGTGTTTCAAGCCTGAGTGTGAAAATTAGAGTAATGCCTTCTAGCTTTTTTCTGCTGTTGCGGTTTTTCC
TGAGAATTGATGGGGTGTTTATCAGAATGAACTACACGAGACTTTACCATGAGGCAGACAAGACCTACATGTTAGGAGAA
TACACATCAGGAGAGAGCAAAATTGCTAATTTAATGCATGTCCCACCTTCCCTGTTCACGGAACCTAATGAAATATCACA
GTATTTACCAATAAAGGAGGCAGTTTGTGAGAAGCTGATATTTCCAGAAAGAATGGATCCTAACCCTGCAGACTCACAAG
AATGTACACCTGTGGAA

Alignment

ORF - retro_itri_1756 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 93.09 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MMIHGFQSSHQDFSFGP-WKLTASKTHIMKSADVEXLADELHMPSLPEMMFGDNVLRIQHCSGFGIEFNA
          M.IHGFQSSHQDFSF.P.WKLTASKT.IMKSADVE.LADELHMPSLPEMMFGDNV.RIQH.SGFGIEFNA
Retrocopy MIIHGFQSSHQDFSFRP<WKLTASKTRIMKSADVERLADELHMPSLPEMMFGDNVIRIQHGSGFGIEFNA

Parental  TDALRCVNNYQG-MLK-VACAEEWQESRTEGEHSKEVIKPYDWTYTTDYKGTLLGESLKLKVVPTTDHID
          TDALRCVNNY.G..LK.VAC.EEWQESRTEGEHSKEVIKPYD.TY.TDYK.TLLGESLKLKVVPTTDHID
Retrocopy TDALRCVNNYEGECLK<VACGEEWQESRTEGEHSKEVIKPYD*TYKTDYKKTLLGESLKLKVVPTTDHID

Parental  TEKLKAREQIKFFEEVLLFEDELHDHGVSSLSVKIRVMPSSFFLLLRFFLRIDGVLIRMNDTRLYHEADK
          TEKLKAREQIKFFEEVLLFEDELHDHGVSSLSVKIRVMPSSFFLLLRFFLRIDGV.IRMN.TRLYHEADK
Retrocopy TEKLKAREQIKFFEEVLLFEDELHDHGVSSLSVKIRVMPSSFFLLLRFFLRIDGVFIRMNYTRLYHEADK

Parental  TYMLREYTSRESKIANLMHVPPSLFTEPNEISQYLPIKEAVCEKLIFPERMDPNPADSQECTPVE
          TYML.EYTS.ESKIANLMHVPPSLFTEPNEISQYLPIKEAVCEKLIFPERMDPNPADSQECTPVE
Retrocopy TYMLGEYTSGESKIANLMHVPPSLFTEPNEISQYLPIKEAVCEKLIFPERMDPNPADSQECTPVE

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_1756 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_1756 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 13 parental genes, and 19 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000008689	3 retrocopies	retro_chof_1079, retro_chof_1094, retro_chof_1746,
Cavia porcellus	ENSCPOG00000009945	1 retrocopy	retro_cpor_763,
Echinops telfairi	ENSETEG00000005808	1 retrocopy	retro_etel_1273,
Microcebus murinus	ENSMICG00000007808	1 retrocopy	retro_mmur_1335,
Myotis lucifugus	ENSMLUG00000011927	3 retrocopies	retro_mluc_607, retro_mluc_909, retro_mluc_941,
Monodelphis domestica	ENSMODG00000002880	1 retrocopy	retro_mdom_180,
Mus musculus	ENSMUSG00000040843	1 retrocopy	retro_mmus_2653,
Ochotona princeps	ENSOPRG00000011313	1 retrocopy	retro_opri_885,
Pteropus vampyrus	ENSPVAG00000005071	1 retrocopy	retro_pvam_257,
Rattus norvegicus	ENSRNOG00000003048	1 retrocopy	retro_rnor_2197,
Sarcophilus harrisii	ENSSHAG00000018932	1 retrocopy	retro_shar_771,
Ictidomys tridecemlineatus	ENSSTOG00000014921	1 retrocopy	retro_itri_1756 ,
Tupaia belangeri	ENSTBEG00000017081	3 retrocopies	retro_tbel_1717, retro_tbel_2833, retro_tbel_3376,