RetrogeneDB ID: retro_itri_241

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393281.1:13767701..13768164(+)
• Located in intron of: ENSSTOG00000020671

Retrocopy information

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

Parental gene information

• Parental gene symbol: MOCS2
• Ensembl ID: ENSSTOG00000010607
• Aliases: None
• Description: molybdenum cofactor synthesis 2 [Source:HGNC Symbol;Acc:7193]

Sequence

>retro_itri_241
TCTAGAAAAGATATGGACAAAGTTGAAGAGACATCTAAAGACATAATAAAATTACTGCTGAGAAACTTTCTGTGGATGAT
GTCTCCCAGTTAGTGACATCTCCTCTCTGTGGGGCAATATCCCTATTTGTAGGGACTACAAGAAATAACTTTGAAGGAAA
AAAAGTCATTAGCTTAGAATATGAAGCATATCTACCAATGGCAGAAAATGAAATCAGAAAAATTTGTAGTGACATTAGGC
AGAAATGGCCAGTGAAGCACATAGCAGTGTTCCATAGACTTGGTTTGGTTCCAGTGTCTGAAGCAAGCATAATTATTGCT
GTGTCCTCAGCCCACAGGGCTGCATCCTTGAAGCTGTCACCTATGCCATTGACACTTTAAAAGCCAGGGTGCCCATATAG
AAAAAGGAACTATATGAAGAATCATCATCATCTTGGAAAAGAAACAAAGAATGCTTTTGGGCA

Alignment

ORF - retro_itri_241 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 97.45 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  SRKDMDKVEETSKDIIKF-TAEKLSVDDVSQLVTSPLCGAISLFVGTTRNNFEGKKVISLEYEAYLPMAE
          SRKDMDKVEETSKDIIK..TAEKLSVDDVSQLVTSPLCGAISLFVGTTRNNFEGKKVISLEYEAYLPMAE
Retrocopy SRKDMDKVEETSKDIIKL<TAEKLSVDDVSQLVTSPLCGAISLFVGTTRNNFEGKKVISLEYEAYLPMAE

Parental  NEIRKICSDIRQKWPVKHIAVFHRLGLVPVSEASIIIAVSSAHRAASL-EAVTYAIDTLKARVPIWKKEL
          NEIRKICSDIRQKWPVKHIAVFHRLGLVPVSEASIIIAVSSAHRAASL.EAVTYAIDTLKARVPI.KKEL
Retrocopy NEIRKICSDIRQKWPVKHIAVFHRLGLVPVSEASIIIAVSSAHRAASL<EAVTYAIDTLKARVPI*KKEL

Parental  YEESSSSWKRNKECFWA
          YEESSSSWKRNKECFWA
Retrocopy YEESSSSWKRNKECFWA

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_241 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_241 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 10 parental genes, and 13 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000005380	1 retrocopy	retro_btau_487,
Cavia porcellus	ENSCPOG00000015752	2 retrocopies	retro_cpor_746, retro_cpor_748,
Macaca mulatta	ENSMMUG00000020449	1 retrocopy	retro_mmul_581,
Monodelphis domestica	ENSMODG00000019459	1 retrocopy	retro_mdom_1654,
Oryctolagus cuniculus	ENSOCUG00000011406	1 retrocopy	retro_ocun_575,
Otolemur garnettii	ENSOGAG00000011108	1 retrocopy	retro_ogar_2170,
Pteropus vampyrus	ENSPVAG00000010175	1 retrocopy	retro_pvam_633,
Ictidomys tridecemlineatus	ENSSTOG00000010607	1 retrocopy	retro_itri_241 ,
Tupaia belangeri	ENSTBEG00000008942	3 retrocopies	retro_tbel_1128, retro_tbel_216, retro_tbel_3310,
Tarsius syrichta	ENSTSYG00000001351	1 retrocopy	retro_tsyr_510,