RetrogeneDB ID: retro_itri_1239

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393409.1:4502202..4502883(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

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

Sequence

>retro_itri_1239
CAAGGCGGAGGTTGGGGCTGAAACTGTGGCTGAAGCAAGGCTGAGGATCAGGAGTGGATGCCAGTCACCAAGCTGAGATC
CCTGGCCAAGGACTTGAAGATCTAGTCCATGGAAATCTGGCTCTTCTTTCTGCCCATCAAGGAGTCTGAAGTCATTGACT
TTTTTCTGAGGGCATCACCCAAGGATGAAGTTTCAAGTTCATGCCTGTGCAGAAGCAGACCTGCGCTGGCCAGGGGACCA
GGTGCCAGGCATCTATTGTTATCTGGGACTGCACTGGTCAATAGGGTTGGGAGTTAAGTGCTCCAAGAAGGTAGCCACTG
TTCTCTGAGGGGGCCATCATACTGACCAAATTCCCCATTGTTCCTGTGCAGAGAGGCTACTGGGGGAACAAGATGGGCAA
GCTCCAAACTGTCCCTTGCCAGGTGACAAGCCACTGTGTTTCTGTGTGGGTGTGTCCCATCCCTGCCCCCAGAGGCACTG
GCATCATCTCAGCCCCTGTGTCCAAGAAGCTGCTGCTGCTGCTGGTATTGGTGACTGCTACACTTCTGCCAGGGGCTGCA
TTGCCACCTCGGGCAATTTTGCCAAGGCAATCTTCCATGCCATCTCCAAGACATATAACTCCTGAGCCCCAATCTCTGCA
AAAAGACTGTGTTCACCAGGTCTCCCTATCAGGAATTCATC

Alignment

ORF - retro_itri_1239 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 66.67 %
• Parental protein coverage: 76.08 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  RGRGRGRGARGGKAEDKEWIPVTKLGRLVKDMKIKSLEEIYLFSLPIKESEIIDFFLGASLKDEV-LKIM
          .G.G.G......KAED.EW.PVTKL..L.KD.KI.S.E.I.LF.LPIKESE.IDFFL.AS.KDEV..K.M
Retrocopy QGGGWG*NCG*SKAEDQEWMPVTKLRSLAKDLKI*SME-IWLFFLPIKESEVIDFFLRASPKDEV<FKFM

Parental  PVQKQTRAGQRTRFKAFVAIGDYNGH-VGLGVKCSKEVATAI-RGAIILAKLSIVPVRRGYWGNKIGKPH
          PVQKQT.AGQ.TR..A...I.D..G...GLGVKCSK.VAT....GAIIL.K..IVPV.RGYWGNK.GK..
Retrocopy PVQKQTCAGQGTRCQASIVIWDCTGQ<IGLGVKCSKKVATVL>EGAIILTKFPIVPVQRGYWGNKMGKLQ

Parental  TVPCKVTGRCGSVLVRLIPAPRGTGIVSAPVPKKLLMM-AGIDDCYTSARGCTATLGNFAKATFDAISKT
          TVPC.VT..C.SV.V..IPAPRGTGI.SAPV.KKLL...AGI.DCYTSARGC.AT.GNFAKA.F.AISKT
Retrocopy TVPCQVTSHCVSVWVCPIPAPRGTGIISAPVSKKLLLL<AGIGDCYTSARGCIATSGNFAKAIFHAISKT

Parental  YS-YLTPDLWKETVFTKSPYQVFL
          Y...L.P.L.K.TVFT.SPYQ.F.
Retrocopy YN<LLSPNLCKKTVFTRSPYQEFI

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_1239 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_1239 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,