RetrogeneDB ID: retro_itri_604

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393305.1:4389152..4390359(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: EIF4B
• Ensembl ID: ENSSTOG00000006800
• Aliases: None
• Description: eukaryotic translation initiation factor 4B [Source:HGNC Symbol;Acc:3285]

Sequence

>retro_itri_604
CGACCTGCCACAGACAGCTTTGACGACTCTCCGCCTAGAAGAGGTGATGACCGCTTTGGTGACAAGTATCGAGATCGCTA
TGATTCCGACCGATATCGGGATGGCTATCGAGATGGCTATCGTGATGGCCCACGCCGGGATCGCTATGACGACCGAGGCA
GTAGAGATTATGACAGAGGCTATGATTCCAGGATAGGCAGTGGCAGAAGAGCATTTGGTCGTGGGTACCGAAGGGATGAT
GACCACAGAGGAGGTGGGGACCGTTATGAAGACCGACATGACCGACGAGACGATGGGTCGTGGAGAACCAGAGATGATCA
CTCTCGGGATGATTATAGGCGTGATGATAAGAGGTCCCCCCCAAAGACCTAAACTGAATCTAAAGCCTCAGAGTACTCCT
AAGGAAGATGATTCCTCTGCTAGCACCTCCCAGTCCAGTCGAGCAGCCTCCATCTTTGGAGGGGCAAAACCTGTTGACAC
AGCTGCTAGAGAAAGAGAAGTAGAAGAACGGCTACAGAAGGAGCAGGAGAAATTGCAGCGCCAGTTGGATGAGCCAAAAC
TAGAACGGCGGCCTAGGGAGAGACACCCAAGCTGGCGAAGTGAAGAAACTCAGGAATGGGAACGGTCAAGGACAGAAAGT
GAGTCATCACAGACTGGAACCTCAGCCACATCTGGCAGAAATGCACGAAGGAGAGAGAGTGAGAAGTCTCTAGAAAATGA
AACACTCAATAAGGAGGAAGACTGTCACTCTCCAACTTCTAAGCCTCCCAAACCTGATCAGCCTCTAAAGGTAATGCCAG
CCCCTCCACCAAAGGAGAATGCGTGGGTGAAGCGAAGTTCTAACCCTCCTGCTCGATCTCAGAGCTCAGACACAGAGCAA
CAATCCCCCACAAGTGGTGGGGGGAAAGTAGCTCCAGCTCAGCCATCTGAGGAAGGACCCACAAGGAAAGATGATAATAA
AATAAATGGAATGAGTGTCCCAAAAGGCCAAACTGGGAACTCCAGCCGTGGTCCAGGAGATGGAGGGAACAAAGATCACT
GGAAGGAGTCAGATAGGAAAGAGGGCAAAAAGGATCAAGACTCCAGATCTGCACCTGAGCCAAAGAAACCTGAGGAAAAT
CCAGCCTCTAAGTTCAGTTCTGCAAGCAAGTATGCCGCTCTCTCTGAGGATGGTGAAGATGAAAATGAGGGAGAAGACTA
CACTGAG

Alignment

ORF - retro_itri_604 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 79.23 %
• Parental protein coverage: 71.58 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  RIRVDVADQAQDKDRDDRSFGRDRNRDSDKTDTDWRARPATDSFDDYPPRRGDDSFGDKYRDRYDSDRYR
          R...D..D.......DDR.FG.D..RD....D.D.............P.R...D..G....DR....R..
Retrocopy RPATDSFDDSPPRRGDDR-FG-DKYRD--RYDSDRXXXXXXXXXXXXPRRDRYDDRGSRDYDRGYDSRIG

Parental  DGYRDGYRDGPRRDMDRYGDRGGGDRYEDRYDRRDDRSWSSRDDYSRDDYRRDD-RGPPQRPKLNLKPRS
          .G.R.....G.RRD.D....RGGGDRYEDR.DRRDD.SW..RDD.SRDDYRRDD.RGPPQRPKLNLKP.S
Retrocopy SGRR-AFGRGYRRDDDH---RGGGDRYEDRHDRRDDGSWRTRDDHSRDDYRRDD>RGPPQRPKLNLKPQS

Parental  TPKEDDSSASTSQSSRAASIFGGAKPVDTAAREREVEERLQKEQEKLQRQLDEPNIFKSLLYRHPSWRSE
          TPKEDDSSASTSQSSRAASIFGGAKPVDTAAREREVEERLQKEQEKLQRQLDEP........RHPSWRSE
Retrocopy TPKEDDSSASTSQSSRAASIFGGAKPVDTAAREREVEERLQKEQEKLQRQLDEPKLERRPRERHPSWRSE

Parental  ETQERERSRTGSESSQTGTSATSGRNARRRESEKSLENETLNKEEDCHSPTSKPPKPDQPLKVMPAPPPK
          ETQE.ERSRT.SESSQTGTSATSGRNARRRESEKSLENETLNKEEDCHSPTSKPPKPDQPLKVMPAPPPK
Retrocopy ETQEWERSRTESESSQTGTSATSGRNARRRESEKSLENETLNKEEDCHSPTSKPPKPDQPLKVMPAPPPK

Parental  ENAWVKRSSNPPARSQSSDTEQQSPTSGGGKVAPAQPSEEGPTRKAQADDNKIDGMSVPKGQTGNSSRGP
          ENAWVKRSSNPPARSQSSDTEQQSPTSGGGKVAPAQPSEEGPTRK...DDNKI.GMSVPKGQTGNSSRGP
Retrocopy ENAWVKRSSNPPARSQSSDTEQQSPTSGGGKVAPAQPSEEGPTRK---DDNKINGMSVPKGQTGNSSRGP

Parental  GDGGNKDHWKESDRKESKKDQDSRSAPEPKKPEENPASKFSSASKYAALSVDGEDENEGEDYTE
          GDGGNKDHWKESDRKE.KKDQDSRSAPEPKKPEENPASKFSSASKYAALS.DGEDENEGEDYTE
Retrocopy GDGGNKDHWKESDRKEGKKDQDSRSAPEPKKPEENPASKFSSASKYAALSEDGEDENEGEDYTE

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_604 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_604 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 13 parental genes, and 41 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000018176	2 retrocopies	retro_cjac_1717, retro_cjac_2001,
Cavia porcellus	ENSCPOG00000005595	3 retrocopies	retro_cpor_278, retro_cpor_752, retro_cpor_937,
Homo sapiens	ENSG00000063046	7 retrocopies	retro_hsap_1686, retro_hsap_2639, retro_hsap_2698, retro_hsap_3767, retro_hsap_4196, retro_hsap_4848, retro_hsap_4891,
Gorilla gorilla	ENSGGOG00000013695	5 retrocopies	retro_ggor_1233, retro_ggor_1263, retro_ggor_1882, retro_ggor_1883, retro_ggor_3024,
Loxodonta africana	ENSLAFG00000009534	1 retrocopy	retro_lafr_294,
Macropus eugenii	ENSMEUG00000012341	2 retrocopies	retro_meug_1054, retro_meug_585,
Macaca mulatta	ENSMMUG00000001062	5 retrocopies	retro_mmul_1428, retro_mmul_2384, retro_mmul_2589, retro_mmul_731, retro_mmul_783,
Mus musculus	ENSMUSG00000058655	1 retrocopy	retro_mmus_3686,
Nomascus leucogenys	ENSNLEG00000017727	3 retrocopies	retro_nleu_2371, retro_nleu_2601, retro_nleu_721,
Pongo abelii	ENSPPYG00000025848	7 retrocopies	retro_pabe_1388, retro_pabe_1560, retro_pabe_2283, retro_pabe_260, retro_pabe_3532, retro_pabe_3768, retro_pabe_506,
Rattus norvegicus	ENSRNOG00000010103	2 retrocopies	retro_rnor_2467, retro_rnor_2972,
Ictidomys tridecemlineatus	ENSSTOG00000006800	1 retrocopy	retro_itri_604 ,
Tupaia belangeri	ENSTBEG00000005423	2 retrocopies	retro_tbel_2363, retro_tbel_4167,