RetrogeneDB ID: retro_itri_283

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393282.1:2243878..2244277(+)
• Located in intron of: ENSSTOG00000008251

Retrocopy information

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

Parental gene information

• Parental gene symbol: RPL27
• Ensembl ID: ENSSTOG00000020555
• Aliases: None
• Description: ribosomal protein L27 [Source:HGNC Symbol;Acc:10328]

Sequence

>retro_itri_283
AAGTTCACGAAACCCAGGAAGGTGGTGTTGGTCCTGGCCGGACGCTTCTCTGGACGCAAAGCTATCATTGTGAAGAACAT
TGATGATGGCACATCAGACTGTCCCTATAGCCATGCTCTGGTGGCTGGAATCGACCGCTATCCCCACAAAGTGACGGCTG
CCCTGGGCAAGAAGAAAATTGCCAAAAGGTCCAAGGTGAAGTCTTTTGTGAAGGTTTATAACTACAGTCACCTCCTGCCC
ACAGGTGCTCTGTGGGTATCCCCTGGACAAAACTGTCATCAACAGGATGTCTTTAGAGAGCCTGCTCATAGACGTAAGGC
CAGTAGGAAGACCAAGGTGAAGTTTGACGAGAGGTACAAGATGGGCAAGAACAAATGGTTCTTCCAGAGCTTCAGTTTT

Alignment

ORF - retro_itri_283 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 78.83 %
• Parental protein coverage: 98.53 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  KFMKPGKVVLVLAGRYSGRKAVIVKNIDDGTSDRPYSHALVAGIDRYPRKVTAAMGKKKIAKRSKIKSFV
          KF.KP.KVVLVLAGR.SGRKA.IVKNIDDGTSD.PYSHALVAGIDRYP.KVTAA.GKKKIAKRSK.KSFV
Retrocopy KFTKPRKVVLVLAGRFSGRKAIIVKNIDDGTSDCPYSHALVAGIDRYPHKVTAALGKKKIAKRSKVKSFV

Parental  KVYNYNHLMPT-RYSVDI-PLDKTVVNK-DVFRDPALKRKARREAKIKFEERYKTGKNKWFFQKLRF
          KVYNY.HL.PT.R.SV.I.PLDKTV.N..DVFR.PA..RKA.R..K.KF.ERYK.GKNKWFFQ...F
Retrocopy KVYNYSHLLPT<RCSVGI<PLDKTVINR<DVFREPAHRRKASRKTKVKFDERYKMGKNKWFFQSFSF

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_283 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_283 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 18 parental genes, and 80 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000000200	3 retrocopies	retro_amel_122, retro_amel_37, retro_amel_674,
Bos taurus	ENSBTAG00000017441	6 retrocopies	retro_btau_1113, retro_btau_129, retro_btau_1565, retro_btau_1855, retro_btau_338, retro_btau_394,
Canis familiaris	ENSCAFG00000014630	6 retrocopies	retro_cfam_1193, retro_cfam_2109, retro_cfam_339, retro_cfam_364, retro_cfam_947, retro_cfam_959,
Callithrix jacchus	ENSCJAG00000013067	9 retrocopies	retro_cjac_1345, retro_cjac_1350, retro_cjac_1543, retro_cjac_1630, retro_cjac_2210, retro_cjac_275, retro_cjac_2828, retro_cjac_369, retro_cjac_776,
Dipodomys ordii	ENSDORG00000010907	6 retrocopies	retro_dord_154, retro_dord_335, retro_dord_477, retro_dord_527, retro_dord_601, retro_dord_784,
Felis catus	ENSFCAG00000013142	6 retrocopies	retro_fcat_1026, retro_fcat_1184, retro_fcat_1824, retro_fcat_228, retro_fcat_698, retro_fcat_78,
Gorilla gorilla	ENSGGOG00000026039	6 retrocopies	retro_ggor_1741, retro_ggor_1852, retro_ggor_2546, retro_ggor_2630, retro_ggor_298, retro_ggor_907,
Loxodonta africana	ENSLAFG00000014220	3 retrocopies	retro_lafr_443, retro_lafr_739, retro_lafr_965,
Myotis lucifugus	ENSMLUG00000004119	1 retrocopy	retro_mluc_359,
Macaca mulatta	ENSMMUG00000008090	7 retrocopies	retro_mmul_1646, retro_mmul_1997, retro_mmul_418, retro_mmul_478, retro_mmul_52, retro_mmul_680, retro_mmul_925,
Monodelphis domestica	ENSMODG00000015128	1 retrocopy	retro_mdom_1141,
Mus musculus	ENSMUSG00000063316	2 retrocopies	retro_mmus_223, retro_mmus_277,
Nomascus leucogenys	ENSNLEG00000011901	2 retrocopies	retro_nleu_334, retro_nleu_45,
Oryctolagus cuniculus	ENSOCUG00000003872	1 retrocopy	retro_ocun_263,
Pteropus vampyrus	ENSPVAG00000008817	4 retrocopies	retro_pvam_1084, retro_pvam_1231, retro_pvam_25, retro_pvam_509,
Rattus norvegicus	ENSRNOG00000020674	8 retrocopies	retro_rnor_1150, retro_rnor_125, retro_rnor_1257, retro_rnor_1968, retro_rnor_2594, retro_rnor_2989, retro_rnor_386, retro_rnor_414,
Sarcophilus harrisii	ENSSHAG00000012042	4 retrocopies	retro_shar_10, retro_shar_253, retro_shar_730, retro_shar_741,
Ictidomys tridecemlineatus	ENSSTOG00000020555	5 retrocopies	retro_itri_1295, retro_itri_1812, retro_itri_283 , retro_itri_836, retro_itri_926,