RetrogeneDB ID: retro_itri_549

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393300.1:16079458..16080105(-)
• Located in intron of: ENSSTOG00000012682

Retrocopy information

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

Parental gene information

• Parental gene symbol: MRPL19
• Ensembl ID: ENSSTOG00000002873
• Aliases: None
• Description: mitochondrial ribosomal protein L19 [Source:HGNC Symbol;Acc:14052]

Sequence

>retro_itri_549
CTTGAGTTGGAATTTATTCCTCCATGGGAAAAAACAAATCCTGAAATTTCCAATAGAGAGGGAAAATATGTTACAATGAA
GAAGAGCTTGCTCCACGTTCCAGTTCTATGTTGGAAGCATAGTCTACGTTTTACCACAGCCAGCCCAAGTGCCCATGGAA
TCACCAGCCAGTTTCTGGGGATATGCATTCAGACATCAGGAAAAGGACTTGGTGTTGCTTTTATCCTGAGGGATCATATT
GAAGGACATGCTGTTGAAAAAAATTTTTGACCTGTATAATCCTCAAATCTATAAGATCCAAGTGGTCAACTTAGAGAAAT
GCCAGATGGTAGCCTAGGATACTGACAACATGCCCTTCTTGAAAACCACACTTTAGATTTGAAGATGAAACCGGCGCTAT
CAGAGCCTCATCAAGAGGGTCTGTTAATGAGCTAAAAGTAAAAATGAGGCCTTGTAAGTCCTGGTCCAAACACTGGAAAT
GCCAAGATTTGCATATTAAAGGAATTATATTTGATCTTTGCGTAACTAAAGAACACATGAAAGAAAGTCAGAAGTGCAGT
CAGCCACTGTTTGAGTTTGATATGATACGGGAATTTGATACTTCAAAACCTGAAGCTGCAAAATGGGATGAAATTGAAGC
ATCAAAA

Alignment

ORF - retro_itri_549 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 55.25 %
• Parental protein coverage: 76.79 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  LSPEFIPPRGRTNPLKFQVERRDMLERRKVLHIPEFYVGSILRVTTADPYASGKISQFLGICIHRSGKGL
          L..EFIPP...TNP.....E..........LH.P.......LR.TTA.P.A.G..SQFLGICI..SGKGL
Retrocopy LELEFIPPWEKTNPEISNREGKYVTMKKSLLHVPVLCWKHSLRFTTASPSAHGITSQFLGICIQTSGKGL

Parental  GATFILRNTIEGQGVEI-CFELYNPRIHEIQVIKLEK-RLDDSLLYLRDALPEYSTFDMNMKPVTLE-SS
          G..FILR..IEG..VE...F.LYNP.I..IQV..LEK...D.SL.Y...AL.E..T.D..MKP...E..S
Retrocopy GVAFILRDHIEGHAVEK>IFDLYNPQIYKIQVVNLEK<MPDGSLGY*QHALLENHTLDLKMKPALSE<AS

Parental  KEIPVNMLKVKMKP-KPWSKRWERPYFNIKGIRFDLCLTEEQMKEAQKWSQPWLEFDMMREYDTSKIEAA
          ....VN.LKVKM.P.K.WSK.W......IKGI.FDLC.T.E.MKE.QK.SQP..EFDM.RE.DTSK.EAA
Retrocopy SRGSVNELKVKMRPCKSWSKHWKCQDLHIKGIIFDLCVTKEHMKESQKCSQPLFEFDMIREFDTSKPEAA

Parental  IWEEIEASK
          .W.EIEASK
Retrocopy KWDEIEASK

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_549 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_549 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 9 parental genes, and 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Erinaceus europaeus	ENSEEUG00000002266	1 retrocopy	retro_eeur_485,
Homo sapiens	ENSG00000115364	1 retrocopy	retro_hsap_2957,
Gorilla gorilla	ENSGGOG00000027896	1 retrocopy	retro_ggor_2048,
Loxodonta africana	ENSLAFG00000000146	1 retrocopy	retro_lafr_472,
Myotis lucifugus	ENSMLUG00000012774	1 retrocopy	retro_mluc_1308,
Pongo abelii	ENSPPYG00000012255	1 retrocopy	retro_pabe_2453,
Pan troglodytes	ENSPTRG00000012108	1 retrocopy	retro_ptro_2002,
Ictidomys tridecemlineatus	ENSSTOG00000002873	1 retrocopy	retro_itri_549 ,
Tupaia belangeri	ENSTBEG00000016470	1 retrocopy	retro_tbel_326,