RetrogeneDB ID: retro_itri_1855

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH394176.1:4874..5310(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSSTOG00000015375
• Aliases: None
• Description: None

Sequence

>retro_itri_1855
GTCAGTTTTGTATTAATATTAAAAAATGAGCACTTCACCACTGCTTCATCTCTGAAGTCTCAGAGCCGCCTTTTCTGCTT
TCCTGAGTTCTAGTGGAGGGATAACAGGAAGCGAGAGCGATGATTCTGATGAATGTTCAGTTGTGGGAGTCGGGATGAAT
TGCCTGCGAGTGCTTCTGGCGTACAACAGAGAAAATGCCAGAAGACGCCCAACAAGCTAGCAAGGGAAGAAAATGCTCCA
AAGGGAGGGCCAGAAGCAGTTTACTCAGAACAGACTCAGAGACAATTGTACCTCCTGGGAAAAGCAAGTACTTGTGGAAA
GCAAAATAAGAAGGCATGAGGACCCAGGAAGGAAAGAGTGAGTTATCTGGAGCCACAGGATGCTGATAAGGAAGTGTCTC
CAGGCATAGGAAGAGACCAGCAGCCCTGAGGAAGAA

Alignment

ORF - retro_itri_1855 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 58.39 %
• Parental protein coverage: 75.79 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  ITYVYLKRN--YTTMTSL-GLRATLPAFMSSNRQIIESQSDDSDECR-NRGSQDELPKSASGIRQRKRKE
          ...V....N...TT..SL..LRA...AF.SS...I..S.SDDSDEC....GS.DELP.SASG..QRK...
Retrocopy VSFVLILKNEHFTTASSL>SLRAAFSAFLSSSGGITGSESDDSDECS<SCGSRDELPASASGVQQRKC-Q

Parental  KMPKKPAMEENDPKGVPKAVGSEQAQRQLYPLGKASTSGKQSEKVSGPRKKNVN-IWSHRLRERKYLVAY
          K.P.K.A.EEN.PKG.P.AV.SEQ.QRQLY.LGKAST.GKQ..K..GPRK..V..IWSHR...RK.L.A.
Retrocopy KTPNKLAREENAPKGGPEAVYSEQTQRQLYLLGKASTCGKQNKKA*GPRKERVS>IWSHRMLIRKCLQA*

Parental  EEISDPEEE
          EE.S.PEEE
Retrocopy EETSSPEEE

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_1855 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_1855 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 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000014776	1 retrocopy	retro_cjac_2373,
Homo sapiens	ENSG00000204645	1 retrocopy	retro_hsap_3512,
Gorilla gorilla	ENSGGOG00000026107	1 retrocopy	retro_ggor_2374,
Macaca mulatta	ENSMMUG00000019164	1 retrocopy	retro_mmul_1862,
Nomascus leucogenys	ENSNLEG00000003504	1 retrocopy	retro_nleu_482,
Pongo abelii	ENSPPYG00000020365	1 retrocopy	retro_pabe_2903,
Pan troglodytes	ENSPTRG00000021857	1 retrocopy	retro_ptro_2385,
Ictidomys tridecemlineatus	ENSSTOG00000015375	3 retrocopies	retro_itri_1394, retro_itri_1855 , retro_itri_746,