RetrogeneDB ID: retro_itri_1851

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH394117.1:41222..41834(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSSTOG00000014416
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: NFYB
• Ensembl ID: ENSSTOG00000005279
• Aliases: None
• Description: nuclear transcription factor Y, beta [Source:HGNC Symbol;Acc:7805]

Sequence

>retro_itri_1851
ATGGATGGTGACAGTTCTACAGATGCTACCCAACTAGGAATTTCTGCAGACTACATTGGAGGAAGTCATTATGTGATACA
GCCTCACGATAATACTGAGGACAGCATGAATGATCATGAAGATACAAATGGTTCAAAAGAAAGTTTCAGAGAACAAGATA
TATATCTTCCAATTGCAAACGTGGCTAGGATAATGAAAAATGCTATACCTCAAACAGGAAAGATTGCAAAAGATGCCAAA
GAATGTGTGCAGGAATGTGTGAGTGAGTTCATAAGCTTTATAACATCAGAGGCAAGTGAAAGATGCCATCAAGAGAAGCG
GAAGACAATCAATGGAGAGGATATTCTCTTTGCCATGTCTACCTTAGACTTTGACAGTTATGCAGAACCTCTGAAATTAT
ATCTTCAGAAATTCAGAGAGGCTATGAAAGGAGAGAAGGGAATTGGTGGGGCAGTCACAGCTACAGATGGACTAAGTGAA
GAACTTACAGAGGAGGCATTTACAAACCAGTTACCAGCTGGCTTAATAACTGCAGATGGTCAACAACAAAATGTTATGGT
TTACACAACGTCCTATCAACAGATTTCTGGTGTTCAACAAATTCAGTTTTCA

Alignment

ORF - retro_itri_1851 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 97.56 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MDGDSSTTDATQLGISADYIGGSHYVIQPHDDTEDSMNDHEDTNGSKESFREQDIYLPIANVARI-KNAI
          MDGDSST.DATQLGISADYIGGSHYVIQPHD.TEDSMNDHEDTNGSKESFREQDIYLPIANVARI.KNAI
Retrocopy MDGDSST-DATQLGISADYIGGSHYVIQPHDNTEDSMNDHEDTNGSKESFREQDIYLPIANVARIMKNAI

Parental  PQTGKIAKDAKECVQECVSEFISFITSEASERCHQEKRKTINGEDILFAMSTLGFDSYVEPLKLYLQKFR
          PQTGKIAKDAKECVQECVSEFISFITSEASERCHQEKRKTINGEDILFAMSTL.FDSY.EPLKLYLQKFR
Retrocopy PQTGKIAKDAKECVQECVSEFISFITSEASERCHQEKRKTINGEDILFAMSTLDFDSYAEPLKLYLQKFR

Parental  EAMKGEKGIGGAVTATDGLSEELTEEAFTNQLPAGLITADGQQQNVMVYTTSYQQISGVQQIQFS
          EAMKGEKGIGGAVTATDGLSEELTEEAFTNQLPAGLITADGQQQNVMVYTTSYQQISGVQQIQFS
Retrocopy EAMKGEKGIGGAVTATDGLSEELTEEAFTNQLPAGLITADGQQQNVMVYTTSYQQISGVQQIQFS

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_1851 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_1851 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 17 parental genes, and 27 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000006686	1 retrocopy	retro_amel_940,
Bos taurus	ENSBTAG00000030744	1 retrocopy	retro_btau_1681,
Canis familiaris	ENSCAFG00000029177	1 retrocopy	retro_cfam_1677,
Callithrix jacchus	ENSCJAG00000014610	1 retrocopy	retro_cjac_1133,
Cavia porcellus	ENSCPOG00000003213	1 retrocopy	retro_cpor_901,
Felis catus	ENSFCAG00000026471	1 retrocopy	retro_fcat_207,
Homo sapiens	ENSG00000120837	2 retrocopies	retro_hsap_2827, retro_hsap_4047,
Gorilla gorilla	ENSGGOG00000008866	1 retrocopy	retro_ggor_2714,
Myotis lucifugus	ENSMLUG00000005468	1 retrocopy	retro_mluc_1764,
Macaca mulatta	ENSMMUG00000022570	3 retrocopies	retro_mmul_1433, retro_mmul_2119, retro_mmul_2335,
Mustela putorius furo	ENSMPUG00000012064	3 retrocopies	retro_mputfur_1531, retro_mputfur_1563, retro_mputfur_1567,
Nomascus leucogenys	ENSNLEG00000006543	2 retrocopies	retro_nleu_1203, retro_nleu_2061,
Oryctolagus cuniculus	ENSOCUG00000004415	4 retrocopies	retro_ocun_1334, retro_ocun_1816, retro_ocun_1824, retro_ocun_1845,
Ochotona princeps	ENSOPRG00000008117	2 retrocopies	retro_opri_36, retro_opri_657,
Ictidomys tridecemlineatus	ENSSTOG00000005279	1 retrocopy	retro_itri_1851 ,
Ictidomys tridecemlineatus	ENSSTOG00000027365	1 retrocopy	retro_itri_866,
Tupaia belangeri	ENSTBEG00000005731	1 retrocopy	retro_tbel_4360,