RetrogeneDB ID: retro_itri_178

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: AGTP01143534.1:3217..3719(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RPL19
• Ensembl ID: ENSSTOG00000011120
• Aliases: None
• Description: ribosomal protein L19 [Source:HGNC Symbol;Acc:10312]

Sequence

>retro_itri_178
AGAGGTGCCTCCAGTTTCCCTTGCTGTGGCAAAAGAAGCTTTGGTTGGATCCCAATGAAACCAATGAAATCTTCAATGCC
AACTCTCATCAGCAGATTTGGAAGCTGATCAAAGATAGCTGATCATCCACAAAACCAGTGACTATTCATTCTGAGGCTCC
ATGCCAGAAAAATTCTTTGGCTCCCCAGAGACACAGGCATGTGGGCATAGGTAAGCAGAAGAGTATAGTTAATGCTCCAA
TGCAGGAGAAGGTCACCTGGGTGAATAGGATGTGAATTCTGTGTAGGATGCTCAGAGATACCATGAATCTAAGATTAACC
ACCACATGTATCACAGCTTCTACCTGAAGGTAAAGGGCAATGTCTGCAAAAACAAGTGGATTGTCATGGAACATATTCTA
AAACTGAAGGCAGATAATGCCAAGAAGAAGCTTCTGGCTGACCAGGCTGAGACCAAAGAGGAATACAAGCTCTGTGAGGA
GCATTCCAGGCTAAAGAGGAGG

Alignment

ORF - retro_itri_178 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 64.91 %
• Parental protein coverage: 86.6 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  RLASSVLRCGK-KKVWLDPNETNEIANANSRQQIRKLIKDGLIIRKPVTVHSRARCRKNTLARRKGRHMG
          R.ASS...CGK.KK.WLDPNETNEI.NANS.QQI.KLIKD.....KPVT.HS.A.C.KN.LA....RH.G
Retrocopy RGASSFPCCGK<KKLWLDPNETNEIFNANSHQQIWKLIKDS*SSTKPVTIHSEAPCQKNSLAPQRHRHVG

Parental  IGKRKGTANARMPEKVTWMRRMRILRRLLR-RYRESKKIDRHMYHSLYLKVKGNVFKNKRILMEHIHKLK
          IGK.K...NA.M.EKVTW..RM.IL.R.LR.RY.ES.KI..HMYHS.YLKVKGNV.KNK.I.MEHI.KLK
Retrocopy IGKQKSIVNAPMQEKVTWVNRM*ILCRMLR<RYHES-KINHHMYHSFYLKVKGNVCKNKWIVMEHILKLK

Parental  ADKARKKLLADQAEARRS-KTKEARKRREER
          AD.A.KKLLADQAE.....K..E...R...R
Retrocopy ADNAKKKLLADQAETKEEYKLCEEHSRLKRR

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_178 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_178 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 8 parental genes, and 104 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000008520	4 retrocopies	retro_cjac_131, retro_cjac_220, retro_cjac_32, retro_cjac_64,
Equus caballus	ENSECAG00000025080	6 retrocopies	retro_ecab_104, retro_ecab_319, retro_ecab_351, retro_ecab_456, retro_ecab_497, retro_ecab_905,
Myotis lucifugus	ENSMLUG00000012555	11 retrocopies	retro_mluc_1149, retro_mluc_1473, retro_mluc_1694, retro_mluc_2032, retro_mluc_2034, retro_mluc_2398, retro_mluc_2400, retro_mluc_2616, retro_mluc_573, retro_mluc_887, retro_mluc_890,
Macaca mulatta	ENSMMUG00000004235	2 retrocopies	retro_mmul_283, retro_mmul_63,
Nomascus leucogenys	ENSNLEG00000000748	19 retrocopies	retro_nleu_1182, retro_nleu_1570, retro_nleu_1602, retro_nleu_1620, retro_nleu_1889, retro_nleu_2171, retro_nleu_2236, retro_nleu_2284, retro_nleu_2335, retro_nleu_2430, retro_nleu_2446, retro_nleu_2538, retro_nleu_2695, retro_nleu_2702, retro_nleu_2735, retro_nleu_3116, retro_nleu_479, retro_nleu_540, retro_nleu_656,
Pongo abelii	ENSPPYG00000008492	20 retrocopies	retro_pabe_1546, retro_pabe_1687, retro_pabe_1709, retro_pabe_1815, retro_pabe_2177, retro_pabe_2300, retro_pabe_2320, retro_pabe_2496, retro_pabe_2625, retro_pabe_2799, retro_pabe_2800, retro_pabe_3166, retro_pabe_3278, retro_pabe_3299, retro_pabe_3513, retro_pabe_3635, retro_pabe_3829, retro_pabe_4, retro_pabe_973, retro_pabe_980,
Rattus norvegicus	ENSRNOG00000004741	37 retrocopies	retro_rnor_1029, retro_rnor_1039, retro_rnor_1295, retro_rnor_1338, retro_rnor_1405, retro_rnor_1440, retro_rnor_1449, retro_rnor_1478, retro_rnor_1512, retro_rnor_1525, retro_rnor_1558, retro_rnor_1577, retro_rnor_1765, retro_rnor_1766, retro_rnor_1795, retro_rnor_1814, retro_rnor_1860, retro_rnor_1885, retro_rnor_1905, retro_rnor_1907, retro_rnor_1970, retro_rnor_1981, retro_rnor_208, retro_rnor_2169, retro_rnor_2522, retro_rnor_2536, retro_rnor_2708, retro_rnor_2773, retro_rnor_2783, retro_rnor_2921, retro_rnor_2943, retro_rnor_326, retro_rnor_426, retro_rnor_434, retro_rnor_464, retro_rnor_465, retro_rnor_829,
Ictidomys tridecemlineatus	ENSSTOG00000011120	5 retrocopies	retro_itri_1174, retro_itri_1180, retro_itri_1330, retro_itri_178 , retro_itri_200,