RetrogeneDB ID: retro_itri_1666

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393619.1:640379..641188(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSSTOG00000008188
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: RPS2
• Ensembl ID: ENSSTOG00000012944
• Aliases: None
• Description: ribosomal protein S2 [Source:HGNC Symbol;Acc:10404]

Sequence

>retro_itri_1666
ATGGCGGATGACGCTGGTGCAGCGGGAGGTCCTAGGGTCCCGGGGTCCCTGGAATGGGTGGCCTCGGCTTCCGCGGAGGC
TTCGGCAGAGTTCTCCGAGGCCGTGGTCGAGGCCGTGGAGGGGGCCGGGGCTGTGGCCGCGGGGCTCGTGGAGGCAAGGC
CGAAGACAAGGAGTGGATCCCTGTCACCAAGCTGGGCCGCCTGGTCAAGGACATGAAGATCAAGTCCCTGGAGGAGATCT
ATCTCTTCTCTATGCCCATCAAGGAGTCTGAGATCATTGACTTTTTCTTGGGAGCATCACTCAAGGATGAGGTTTTGAAG
ATCATGCCTGTACAGAAACAGACTCGTGCTGGCCAGCGGACCAGATTCAAGGCATTTGTAGCTATTGGGGACTACAATGG
TCATATTGGAACGGGAGTAAAATGCTCCAAGGAAGTACCAACTACTATCCGAGGGGCCATCATCCTGGCCAAGCTCTCCA
TCGTTCCTGTGCGGAGAGGCTATTGGGGGAACAAGATTGGCAAGCCTCACACTGTCCCTTGCAAGGTGACAGGACGTTGT
GGTTCTGTGCTGGTACGGCTCATCCCTGCCCCCAGAGGTACTGGCATCGTCTCAGCTCCTGTACCCAAGAAGCTACTCAT
GATGGCTGGTATTGATGACTGCTACACTTCTGCCAGGGGCTGCACTGCCACCTTGGGCAATTTTGCCAAGGCCACCTTTG
ATGCCATCTCCAAGACATACAGCTATTTGACCCCTGATCTCTGGAAAGAGACTGTGTTCACCAAGTCTCCTTATCAGGAA
TTCACTGAC

Alignment

ORF - retro_itri_1666 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 93.75 %
• Parental protein coverage: 90.03 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MADDAGAAGGPG-GPGGPGMGGRGGFRGGFGSGLRGRGRGRGRGRGRGRGARGGKAEDKEWIPVTKLGRL
          MADDAGAAGGP..GPG.PGMGG.G.FRGGFG..LRGRGRGRG.GRG.GRGARGGKAEDKEWIPVTKLGRL
Retrocopy MADDAGAAGGPR<GPGVPGMGGLG-FRGGFGRVLRGRGRGRGGGRGCGRGARGGKAEDKEWIPVTKLGRL

Parental  VKDMKIKSLEEIYLFSLPIKESEIIDFFLGASLKDEVLKIMPVQKQTRAGQRTRFKAFVAIGDYNGHVGL
          VKDMKIKSLEEIYLFS.PIKESEIIDFFLGASLKDEVLKIMPVQKQTRAGQRTRFKAFVAIGDYNGH.G.
Retrocopy VKDMKIKSLEEIYLFSMPIKESEIIDFFLGASLKDEVLKIMPVQKQTRAGQRTRFKAFVAIGDYNGHIGT

Parental  GVKCSKEVATAIRGAIILAKLSIVPVRRGYWGNKIGKPHTVPCKVTGRCGSVLVRLIPAPRGTGIVSAPV
          GVKCSKEV.T.IRGAIILAKLSIVPVRRGYWGNKIGKPHTVPCKVTGRCGSVLVRLIPAPRGTGIVSAPV
Retrocopy GVKCSKEVPTTIRGAIILAKLSIVPVRRGYWGNKIGKPHTVPCKVTGRCGSVLVRLIPAPRGTGIVSAPV

Parental  PKKLLMMAGIDDCYTSARGCTATLGNFAKATFDAISKTYSYLTPDLWKETVFTKSPYQVFLE
          PKKLLMMAGIDDCYTSARGCTATLGNFAKATFDAISKTYSYLTPDLWKETVFTKSPYQ.F..
Retrocopy PKKLLMMAGIDDCYTSARGCTATLGNFAKATFDAISKTYSYLTPDLWKETVFTKSPYQEFTD

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_1666 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_1666 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 6 parental genes, and 14 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000002549	1 retrocopy	retro_acar_57,
Macropus eugenii	ENSMEUG00000004508	2 retrocopies	retro_meug_156, retro_meug_2103,
Monodelphis domestica	ENSMODG00000016077	1 retrocopy	retro_mdom_536,
Nomascus leucogenys	ENSNLEG00000008877	1 retrocopy	retro_nleu_2895,
Sarcophilus harrisii	ENSSHAG00000015213	5 retrocopies	retro_shar_186, retro_shar_288, retro_shar_456, retro_shar_525, retro_shar_783,
Ictidomys tridecemlineatus	ENSSTOG00000012944	4 retrocopies	retro_itri_1239, retro_itri_1666 , retro_itri_1680, retro_itri_221,