RetrogeneDB ID: retro_itri_454

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393292.1:12104952..12105446(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MRPS15
• Ensembl ID: ENSSTOG00000000608
• Aliases: None
• Description: mitochondrial ribosomal protein S15 [Source:HGNC Symbol;Acc:14504]

Sequence

>retro_itri_454
AGATTCTTGTTTTTGGAAATGGCCAACCAGAAAGGGAAGCTAAGAATCAAGCAAGAAGAGTTGATGAACACAGTCATGGC
AAACCCTGAGGACACCAGATCCCTGGAGGCTCAAATTGTTGCCTTGACCATCGAGATCCACAATTATGAATAACACATGC
AGAAACAGGGAAAGGATAAAAGACACAAACGCTATCTACTGATGATCATTGACCAGAGGAAAAAGATGCTCAAAAACCTC
ATAAGAACAATTATGATGTCCTTGAGAAGGCATACAGGGAGGTGGGATCGGGTACACTTTTCCCCTGTCTATTACTAAAA
TGCTCACTGATGGTTTGTGTGCAAGGAGGTTCTGTGCCTTTGGTTTTCCAGGAGGCACAAAAGCTGAAGAAACAAAAAAG
GGATTTTAAAATCTGCAGCCAAGCAGTTCCCAAACAAGAAGACCAGGGGAACCTAGATAGCTCTTCCAAAGCCAGAGCAG
AGATACTCAAAGAA

Alignment

ORF - retro_itri_454 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 68.02 %
• Parental protein coverage: 64.86 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  RLLSLEMANQKEKLKIKQEQLMKKVVENPEDTRSLEARIVALTIKIRNYEEHMQKHRKDKAHKRYLLMSL
          R.L.LEMANQK.KL.IKQE.LM..V..NPEDTRSLEA.IVALTI.I.NYE.HMQK..KDK.HKRYLLM..
Retrocopy RFLFLEMANQKGKLRIKQEELMNTVMANPEDTRSLEAQIVALTIEIHNYE*HMQKQGKDKRHKRYLLMII

Parental  DQRKKMLKNL-RKTNYDVFEKTCREL-GIEYTFP-PLYYRTAHRRFVAKRALCL-RVFQEAKKLKKQKRI
          DQRKKMLKNL..K.NYDV.EK..RE..GI.YTFP.P.YY..AH..FV.K..LCL..VFQEA.KLKKQKR.
Retrocopy DQRKKMLKNL<HKNNYDVLEKAYREV<GIGYTFP<PVYY*NAH*WFVCKEVLCL<LVFQEAQKLKKQKRD

Parental  LKAKAKAAAAPKQDDQENPESSSKACADVLKE
          .K....A...PKQ.DQ.N..SSSKA.A..LKE
Retrocopy FKICSQA--VPKQEDQGNLDSSSKARAEILKE

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_454 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_454 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 19 parental genes, and 26 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000001463	1 retrocopy	retro_amel_1564,
Canis familiaris	ENSCAFG00000030390	1 retrocopy	retro_cfam_1939,
Callithrix jacchus	ENSCJAG00000001852	3 retrocopies	retro_cjac_3095, retro_cjac_761, retro_cjac_859,
Cavia porcellus	ENSCPOG00000010877	1 retrocopy	retro_cpor_430,
Dipodomys ordii	ENSDORG00000007581	1 retrocopy	retro_dord_118,
Felis catus	ENSFCAG00000005265	1 retrocopy	retro_fcat_915,
Homo sapiens	ENSG00000116898	1 retrocopy	retro_hsap_1594,
Myotis lucifugus	ENSMLUG00000006475	1 retrocopy	retro_mluc_1945,
Monodelphis domestica	ENSMODG00000017813	1 retrocopy	retro_mdom_1094,
Mus musculus	ENSMUSG00000028861	1 retrocopy	retro_mmus_3447,
Nomascus leucogenys	ENSNLEG00000011467	1 retrocopy	retro_nleu_615,
Otolemur garnettii	ENSOGAG00000002656	2 retrocopies	retro_ogar_1327, retro_ogar_16,
Pongo abelii	ENSPPYG00000001537	1 retrocopy	retro_pabe_1310,
Pan troglodytes	ENSPTRG00000000541	1 retrocopy	retro_ptro_1071,
Sus scrofa	ENSSSCG00000026393	1 retrocopy	retro_sscr_1190,
Ictidomys tridecemlineatus	ENSSTOG00000000608	1 retrocopy	retro_itri_454 ,
Tupaia belangeri	ENSTBEG00000000958	4 retrocopies	retro_tbel_1633, retro_tbel_4438, retro_tbel_845, retro_tbel_882,
Tarsius syrichta	ENSTSYG00000008948	2 retrocopies	retro_tsyr_1612, retro_tsyr_372,
Tursiops truncatus	ENSTTRG00000002345	1 retrocopy	retro_ttru_1500,