RetrogeneDB ID: retro_itri_206

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393279.1:34437826..34438209(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SEC11A
• Ensembl ID: ENSSTOG00000019948
• Aliases: None
• Description: SEC11 homolog A (S. cerevisiae) [Source:HGNC Symbol;Acc:17718]

Sequence

>retro_itri_206
AATGGCAACATGGAACCTGCATTTCATAGAGGAGATCTCCTTCTATCAAATCTGAGTTGAAACTCCCATATGAGTGGGAG
AAATTGTTGTTTGGGGAATAGAAGGAAAGTCCCGTCACTGAGTTCAGTGAGTCTTAAAGATTCACGAAAAGCAAAATGGG
CATATCAAATTTTTGATCAAAGGAGATAATAATGCTGTTGATGACCAAGGCCTCTATAAACAAGAACAACACCGGCTAGA
GAAAAAAAAGATGTTGTGGTAGAGCCAGAGGATTTGTTCCTTATATTAGAATTGAGAGGATCCTCATGAATGACTATCCT
AAATTTAAGTATGCAGTAGTTTTTTTTTTGTTGTTGGGTTTATTCATGCTGGTCCATCGTGAG

Alignment

ORF - retro_itri_206 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 73.08 %
• Parental protein coverage: 90. %
• Number of stop codons detected: 3
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  SGSMEPAFHRGDLLFLTNR-VEDPIRVGEIVVFRIEGREIPIVHRVLKIHEKQNGHIKFLTKGDNNAVDD
          .G.MEPAFHRGDLL.L.N..VE.PI.VGEIVV..IEG.....V..VLKIHEKQNGHIKFL.KGDNNAVDD
Retrocopy NGNMEPAFHRGDLL-LSNL>VETPI*VGEIVVWGIEGKSRH*VQ*VLKIHEKQNGHIKFLIKGDNNAVDD

Parental  RGLYKQGQHWLEKKDVV-GRARGFVPYIGIVTILMNDYPKFKYAV--LFLLGLFVLVHRE
          .GLYKQ.QH.LE......GRARGFVPYI.I..ILMNDYPKFKYAV....LLGLF.LVHRE
Retrocopy QGLYKQEQHRLEXXXML>GRARGFVPYIRIERILMNDYPKFKYAVXXXXLLGLFMLVHRE

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_206 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_206 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 7 parental genes, and 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Erinaceus europaeus	ENSEEUG00000015328	2 retrocopies	retro_eeur_314, retro_eeur_412,
Macaca mulatta	ENSMMUG00000011486	1 retrocopy	retro_mmul_2343,
Monodelphis domestica	ENSMODG00000019364	1 retrocopy	retro_mdom_726,
Oryctolagus cuniculus	ENSOCUG00000008205	1 retrocopy	retro_ocun_849,
Otolemur garnettii	ENSOGAG00000007281	1 retrocopy	retro_ogar_3315,
Ictidomys tridecemlineatus	ENSSTOG00000019948	1 retrocopy	retro_itri_206 ,
Tupaia belangeri	ENSTBEG00000012320	3 retrocopies	retro_tbel_1139, retro_tbel_2280, retro_tbel_745,