RetrogeneDB ID: retro_itri_263

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393281.1:11741018..11742109(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RFC4
• Ensembl ID: ENSSTOG00000012616
• Aliases: None
• Description: replication factor C (activator 1) 4, 37kDa [Source:HGNC Symbol;Acc:9972]

Sequence

>retro_itri_263
ATGCAGGCATTTCTAAAAGGCACATCTATCAGTACTAAACCACCATTAACCAAGGATCGAGGAGTAGCTGCCACTGCAGG
GAGCAGTGGTGAGAACAAGAAAGTCAAACATGTTCCATGGGTGGAAAAATATCGCCCAAAATGTGTAGATGAAGTTGCTT
TCAAGAAGAAGTAGTTGCAGTGTTGAAAAAATCTTGAGAAGGAGCTGATCTACCTAATCTCTTGTTTTATGGGCCACCTG
GAACTGGGAAGACATCCACCATTTTGGCAGCTGCTAGAGAATTCTTTGGGCCTGAACTATTTCGATTAAGAGTTCTTGAG
TTAAATGCATCTGATGAACGTGGAATACAAGTAGTTCTAGAGAAGGTGAAAAATTTTGCTCAATTAACTGTGTCAGGAAG
TCGTTCAGATGGGAAGCCATGTCCTCCTTTTAAGATTGTAATTTTGGATGAAGCTGATTCCATGACCTCAGCTGCTCAGG
CAGCTTTAAGATGAACTATGGAGAAAGAATCTAAAACCACACGTTTCTGTCTCATCTGTAACTATATTAGTAGAATAATT
GAACCCTTGACCTCTAGATGTTCAAAATTCCACTTCAAGCCTTTATCAGATGAAACTCAACAGCAGCGATTACTAGACAT
TGCTGAGAAGGAAAATGTCAAAATTAGTAATGAGGGAATAGTTTATCTAGTTAAAGTATCAGAGGGAGACTTAAGGAAAG
CCATTACATTTCTTCAAAGTGCTACTCGATTAACAGGTGGAAAGGAAGTCATGGAAAAAGTGATCACAGACATTGCTGGG
GTTATACCAGCTGAGGCAATTGATGGAATATTTGCTGCATGTCAGAGTGGCTCCTTTGATAAACTGGAAGCTGTAGTGAA
GGAATTGATAGATGAGGGTCATGCAGCCACTCAATTTATAAATCAACTCCATGATGTGGTTGTAGAAAATGATAACCTTT
CTGACAAACAGAAGTCCATCATTACAGAAAAGCTTGCGGAAGTTGACAAATGCTTAGCAGATGGCGCTGATGAACACCTG
CAATTGATTGGGCTGTGTGCAACCCTGATGCAGCAATTAACTCAGAACTGT

Alignment

ORF - retro_itri_263 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 96.99 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MQAFLKGTSISTKPPLTKDRGVAATAGSSGENKKVKHVPWVEKYRPKCVDEVAF-QEEVVAVLKKSLEGA
          MQAFLKGTSISTKPPLTKDRGVAATAGSSGENKKVKHVPWVEKYRPKCVDEVAF.QEEVVAVLKKS.EGA
Retrocopy MQAFLKGTSISTKPPLTKDRGVAATAGSSGENKKVKHVPWVEKYRPKCVDEVAF<QEEVVAVLKKS*EGA

Parental  DLPNLLFYGPPGTGKTSTILAAARELFGPELFRLRVLELNASDERGIQVVREKVKNFAQLTVSGSRSDGK
          DLPNLLFYGPPGTGKTSTILAAARE.FGPELFRLRVLELNASDERGIQVV.EKVKNFAQLTVSGSRSDGK
Retrocopy DLPNLLFYGPPGTGKTSTILAAAREFFGPELFRLRVLELNASDERGIQVVLEKVKNFAQLTVSGSRSDGK

Parental  PCPPFKIVILDEADSMTSAAQAALRRTMEKESKTTRFCLICNYISRIIEPLTSRCSKFRFKPLSDKTQQQ
          PCPPFKIVILDEADSMTSAAQAALR.TMEKESKTTRFCLICNYISRIIEPLTSRCSKF.FKPLSD.TQQQ
Retrocopy PCPPFKIVILDEADSMTSAAQAALR*TMEKESKTTRFCLICNYISRIIEPLTSRCSKFHFKPLSDETQQQ

Parental  RLLDIAEKENVKISNEGIAYLVKVSEGDLRKAITFLQSATRLTGGKEVTEKVITDIAGVIPAEAIDGIFA
          RLLDIAEKENVKISNEGI.YLVKVSEGDLRKAITFLQSATRLTGGKEV.EKVITDIAGVIPAEAIDGIFA
Retrocopy RLLDIAEKENVKISNEGIVYLVKVSEGDLRKAITFLQSATRLTGGKEVMEKVITDIAGVIPAEAIDGIFA

Parental  ACQSGSFDKLEAAVKELIDEGHAATQLINQLHDVVVENDNLSDKQKSIITEKLAEVDKCLADGADEHLQL
          ACQSGSFDKLEA.VKELIDEGHAATQ.INQLHDVVVENDNLSDKQKSIITEKLAEVDKCLADGADEHLQL
Retrocopy ACQSGSFDKLEAVVKELIDEGHAATQFINQLHDVVVENDNLSDKQKSIITEKLAEVDKCLADGADEHLQL

Parental  IGLCATLMQQLTQNC
          IGLCATLMQQLTQNC
Retrocopy IGLCATLMQQLTQNC

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_263 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_263 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 3 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Mus musculus	ENSMUSG00000022881	1 retrocopy	retro_mmus_3508,
Ornithorhynchus anatinus	ENSOANG00000020441	1 retrocopy	retro_oana_101,
Ictidomys tridecemlineatus	ENSSTOG00000012616	1 retrocopy	retro_itri_263 ,