RetrogeneDB ID: retro_itri_468

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393293.1:15146676..15147014(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RAB2B
• Ensembl ID: ENSSTOG00000001886
• Aliases: None
• Description: RAB2B, member RAS oncogene family [Source:HGNC Symbol;Acc:20246]

Sequence

>retro_itri_468
ATCAAACAGCAAATCTGGGATACAGACAGGCAAGAATCCTTTCATCTTCCACCTGTTCCTACTACAGGGGAACAGTTGGA
GCATTGCTGGTATATGACATTACAAGACATGAAACCTTCAATCACCTGGCCTCATGGTTAGAGGATGCCCACCAGCATTC
TAGCATGTGGTTTTCATGAAAACTGGGAATAAAGGTGACCTAGAGTCCCACAGGGATGTGAAGAGAGGAGGAGGAAAGGC
CTTTGCTCATGAGCATGACTTACATTCATGGAAACTCAGGCGAAACAGCCTGCAATGTTGAAGAGGCCTTCATTAACACA
AAGAAATCTACAGGAAGA

Alignment

ORF - retro_itri_468 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 71.43 %
• Parental protein coverage: 53.24 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  IKLQIWDTAGQESFR-SITRSYYRGAAGALLVYDITRRETFNHLTSWLEDARQHSSS-NMVIMLIGNKSD
          IK.QIWDT..QESF..S.T.SYYRG..GALLVYDITR.ETFNHL.SWLEDA.QH.SS...V.M..GNK.D
Retrocopy IKQQIWDTDRQESFH<SSTCSYYRGTVGALLVYDITRHETFNHLASWLEDAHQH-SS<HVVFMKTGNKGD

Parental  LESRRDVKREEGEAFAREHG-LIFMETSAK-TACNVEEAFINTAKEIYR
          LES.RDVKR..G.AFA.EH..L.FMET.AK.TACNVEEAFINT.K...R
Retrocopy LESHRDVKRGGGKAFAHEHD<LTFMETQAK<TACNVEEAFINTKKSTGR

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_468 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_468 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 13 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000044207	1 retrocopy	retro_btau_991,
Canis familiaris	ENSCAFG00000005641	1 retrocopy	retro_cfam_1510,
Choloepus hoffmanni	ENSCHOG00000000710	3 retrocopies	retro_chof_2314, retro_chof_706, retro_chof_900,
Cavia porcellus	ENSCPOG00000026575	1 retrocopy	retro_cpor_839,
Macropus eugenii	ENSMEUG00000010489	2 retrocopies	retro_meug_2160, retro_meug_91,
Myotis lucifugus	ENSMLUG00000001902	3 retrocopies	retro_mluc_1243, retro_mluc_1251, retro_mluc_2103,
Sorex araneus	ENSSARG00000004969	1 retrocopy	retro_sara_97,
Ictidomys tridecemlineatus	ENSSTOG00000001886	1 retrocopy	retro_itri_468 ,