RetrogeneDB ID: retro_itri_1431

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393485.1:207855..208334(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CENPN
• Ensembl ID: ENSSTOG00000007345
• Aliases: None
• Description: centromere protein N [Source:HGNC Symbol;Acc:30873]

Sequence

>retro_itri_1431
CAGATGAGTACAGAACCAGATGAAGACATTGATCTTTTTGATGTGGAACAATTCAAACATTCATTCAAGAAAATTCTTCA
GAGAGCATTGAAAAATGTGACGGTCAGCTTCAGAGATGCTGAAGAGAATGCAGTCTGAATTGCCTGGGGAACAAGGTGTA
CAAAGCCAAATCAGTACCAACCCACAACCATGCTGCATTACCCGCAGACTCTCTACGCCTTCCCCTCCTCCCTGCTAAAG
AACATTTTGCCCTCTGGGTCAGGCACTGGCAGTTGCTAGCAAACACCATCAGATGGTGAAAGTGGACCTGAGAAGTCGAT
ACCTGGACTCTCTCAGACTATTGTTTTTAACAGTATAATAAGACCTTTGAAAATCACAACTCTACAACACCTCTACAGGA
AAGATGACTGGGACTAGATGTAAATATGGATTCAAGGATCATTCAGGAAAACACAGTAGAAAAAGACAGAGTCCAAAGA

Alignment

ORF - retro_itri_1431 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 76.51 %
• Parental protein coverage: 51.58 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  QMSKEPDEDVDLFDMEQFKRSFKKILQRALKNVTISFRDAEENAIWIRIAWGTQCTKPNQYKPTYVVHYP
          QMS.EPDED.DLFD.EQFK.SFKKILQRALKNVT.SFRDAEENA..I..AWGT.CTKPNQY.PT...HYP
Retrocopy QMSTEPDEDIDLFDVEQFKHSFKKILQRALKNVTVSFRDAEENAV*I--AWGTRCTKPNQYQPTTMLHYP

Parental  QTPYAFTSSRL-KSIMPLLGQALTVASKHHQIVKMDLRSRHLDSLK-AIVFK-QYDQTFENHNSTTPLQE
          QT.YAF.SS.L.....PL.GQAL.VASKHHQ.VK.DLRSR.LDSL...IVF..QY..TFENHNSTTPLQE
Retrocopy QTLYAFPSSLL>RTFCPL-GQALAVASKHHQMVKVDLRSRYLDSLR<TIVFN<QYNKTFENHNSTTPLQE

Parental  RCLGLDVNMDSRIIHENKVENERVQR
          R.LGLDVNMDSRII.EN.VE..RVQR
Retrocopy R*LGLDVNMDSRIIQENTVEKDRVQR

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_1431 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_1431 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 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000011635	1 retrocopy	retro_btau_1101,
Felis catus	ENSFCAG00000004978	1 retrocopy	retro_fcat_1852,
Homo sapiens	ENSG00000166451	2 retrocopies	retro_hsap_2146, retro_hsap_2291,
Oryctolagus cuniculus	ENSOCUG00000000024	3 retrocopies	retro_ocun_1676, retro_ocun_1806, retro_ocun_528,
Sarcophilus harrisii	ENSSHAG00000002111	1 retrocopy	retro_shar_331,
Ictidomys tridecemlineatus	ENSSTOG00000007345	1 retrocopy	retro_itri_1431 ,
Tupaia belangeri	ENSTBEG00000000039	2 retrocopies	retro_tbel_2049, retro_tbel_3055,