RetrogeneDB ID: retro_itri_889

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393338.1:1897393..1898151(-)
• Located in intron of: ENSSTOG00000009188

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSSTOG00000012459
• Aliases: None
• Description: None

Sequence

>retro_itri_889
ACACTCTCTGTCGGCAACCTTGAAACTAAAGTGACAGAGGAACTACTTTTCAAGCTTTTCCACCAGGATGGGCCAGTAAT
AAAGGTGAAAATTACAAAAGATAAGGATGGTAAACCAAAGCAGTTTGCATTTGTGAATTTCAAACATGAAGTATCTGTTC
CTTATGCTATGAATCTTCTTAATGGAATCAAACTTTTTGAAAGGCCCATCAAAATTCAATTTAGAACAGGAAGTAGTCAT
GCCTCACAGGTTGTCAGTTTGTCATATTCCCAGCATCATGTTGGAAATTCAAGTCCTACTTCTACATCTCCCAGCAGGTA
TGAAAGGATTGTGGATAACATGACAGCATCGGCACAAGTAATACAGAGATCATTTTCTTCTCCAGAAAATTATCAGAGAC
AAACAGTGATGAACAGTGTTTTGAGACAGATGTCATATGGTGGGAAATTTGGGTCTTCACATGTGGATCAGTCAAGATTT
CACCATCAGTTCAGTCACATAATCATACTTTCAACCAGTCTTCAAGCTCCCAGTGACGCCAAGACGCATCACAGCGAAAA
GTCAGACAGAATTCTCATCCCTACCTTTCAGATAGACATTATAGCCGTGAATAGCATTACACCGATCATGGATCTGATCA
TCATTACAGAGGAAACAGAGATGATTTCTTCTATGAAGATAGGAATCATGACGGCTGGAGCCGTGAGTATAAGAGAAGAG
ACAGCAGTAGAGATAGAAAATGGCGCTCCTCTCGACAC

Alignment

ORF - retro_itri_889 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.6 %
• Parental protein coverage: 96.24 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  TLFVGNLETKVTEELLFELFHQLKPEGLRQVVEESAGTHSQFAFVNFKHEVSVPYAMNLLNGIKLFGRPI
          TL.VGNLETKVTEELLF.LFHQ..P...........G...QFAFVNFKHEVSVPYAMNLLNGIKLF.RPI
Retrocopy TLSVGNLETKVTEELLFKLFHQDGPVIKVKITKDKDGKPKQFAFVNFKHEVSVPYAMNLLNGIKLFERPI

Parental  KIQFRSGSSHASQDVSLSYSQHHVGNSSPTSTSPSRYERTVDNVTASAQVIQRSFSSPENYQRQAVMNSV
          KIQFR.GSSHASQ.VSLSYSQHHVGNSSPTSTSPSRYER.VDN.TASAQVIQRSFSSPENYQRQ.VMNSV
Retrocopy KIQFRTGSSHASQVVSLSYSQHHVGNSSPTSTSPSRYERIVDNMTASAQVIQRSFSSPENYQRQTVMNSV

Parental  LRQMSYGGKFGSSHVDQSGF-SPSVQSHNHTFNQSSSSQWRQDSSSSQRKVRQNSHPYLTDRHYSREQRY
          LRQMSYGGKFGSSHVDQS.F.SPSVQSHNHTFNQSSSSQ.RQD...SQRKVRQNSHPYL.DRHYSRE..Y
Retrocopy LRQMSYGGKFGSSHVDQSRF<SPSVQSHNHTFNQSSSSQ*RQD--ASQRKVRQNSHPYLSDRHYSRE*HY

Parental  TDHGSDHHYRGNRDDFFYEDRNHDGWSHEYDNRRDSSRDGKWRSSRH
          TDHGSDHHYRGNRDDFFYEDRNHDGWS.EY..RRDSSRD.KWRSSRH
Retrocopy TDHGSDHHYRGNRDDFFYEDRNHDGWSREY-KRRDSSRDRKWRSSRH

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_889 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_889 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 17 parental genes, and 21 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000013514	1 retrocopy	retro_cfam_1021,
Choloepus hoffmanni	ENSCHOG00000012747	1 retrocopy	retro_chof_570,
Homo sapiens	ENSG00000076053	1 retrocopy	retro_hsap_2283,
Gorilla gorilla	ENSGGOG00000009941	1 retrocopy	retro_ggor_1696,
Loxodonta africana	ENSLAFG00000012444	1 retrocopy	retro_lafr_892,
Myotis lucifugus	ENSMLUG00000023234	2 retrocopies	retro_mluc_1555, retro_mluc_587,
Monodelphis domestica	ENSMODG00000013918	1 retrocopy	retro_mdom_535,
Mus musculus	ENSMUSG00000042396	1 retrocopy	retro_mmus_2436,
Nomascus leucogenys	ENSNLEG00000007323	1 retrocopy	retro_nleu_409,
Oryctolagus cuniculus	ENSOCUG00000003342	1 retrocopy	retro_ocun_924,
Otolemur garnettii	ENSOGAG00000016857	1 retrocopy	retro_ogar_3103,
Pongo abelii	ENSPPYG00000003894	1 retrocopy	retro_pabe_1669,
Pan troglodytes	ENSPTRG00000004305	1 retrocopy	retro_ptro_1617,
Ictidomys tridecemlineatus	ENSSTOG00000000684	2 retrocopies	retro_itri_1153, retro_itri_487,
Ictidomys tridecemlineatus	ENSSTOG00000012459	1 retrocopy	retro_itri_889 ,
Tursiops truncatus	ENSTTRG00000001515	3 retrocopies	retro_ttru_1316, retro_ttru_1441, retro_ttru_478,
Vicugna pacos	ENSVPAG00000006300	1 retrocopy	retro_vpac_311,