RetrogeneDB ID: retro_itri_1104

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393376.1:2762229..2764133(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSSTOG00000021663
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: KIF18B
• Ensembl ID: ENSSTOG00000007553
• Aliases: None
• Description: kinesin family member 18B [Source:HGNC Symbol;Acc:27102]

Sequence

>retro_itri_1104
GGTGTTACCATGGTGATGGCTGTGCAGGACAACATGGTTCAGGTGGTGGTGCGGGTGCGACCCCCCACCTCTCGGGAGTT
GGAGAGTCAGCGGTGGCCTGTGGTTCAAGTGGTGGATGAGCGGGTGCTGGTGTTTGACCCTGAGGAACCTGATGGGGGCC
TCAAATGGGGTGGTACTCATGACGGCCCCAAGAAGAAGGGCAAGGACCTGACATTTGTCTTCGACCGGGTCTTTGGTGAG
AAGGCCACCCAACAGGACATGTTCCAGCACACCACGTGCAGAATCCTGGACAGCTTCCTCCAGGGCTACAACTGTTCAGT
GTTTGCCTATGGGGCTACTGGGGCTGGGAAGACACACACCATGCTGGGAAAGGAGGGGGACCCTGGCATCGTGTACCTGA
CCACCATGGAACTGTACAGGCGTTTTGAGGCCTGCCAGGAGGAGAAGCAATTCGAGGTGCTCATCAGCTACCTGGAGGTG
TACAATGAACAGATCCATGACCTCCTGGAGCCCAAGGGACCCCTAATCATCCGTGAGGACCCTGACAAGGGCGTGGTGGT
GCAAGGACTTTCTTTCCACCAGCCAGCCTCAGCTGAGCAGCTTCTGAAGATGCTGACCAGGGGGAACCACAACCGCACCG
AGCACCCCACAGATGCCAATGCTACTTCCTCCCGCTCCCATGCCATCTTCCAGATCTTTGTAAAGCAACAGGACCGAGTC
CCAGGACTCACTCAGGCCCTGCAGGTGGCCAAGATGAGCCTGATTGACCTGGCTGGCTCAGAGCGGTCATCCAGTAGCGG
TGCCAAGGGGGAGCGACTGCGGGAGGGTGCCAACATCAACCGTTCTTTGCTGGCCCTCATCAATGTCCTCAATGCCCTGG
TGGATGCAAAGGGCCGCAAGTCTCACGTGCCCTACCGAGACAGCAAACTGACCCGCCTGCTGAAGGACTCCATTGGGGGC
AACTGTCGCACAGTGATGATTGCTGCCATCAGCCCCTCTAGCCTGGCCTACAAGGACACTTACAACACCCTCAAATATGC
TGACCGGGCCAAAGAGATCAGACTCACCCTGAAGAGCAACGTGGTCAGTCTGGACTGTCACATCAGCCAGTATGCCACTG
TCTGCCAGCAGCTCCAGGCTGAGGTGGCCTCCCTAAGGAAGAAGCTTCAAGCCTATGAGGCAGGAGCCCAGGCCCCACAG
CAGGGCCTCCCACAGCCCCCCAAGTTGAGCCCTCAACAGCAACACCTTCCTAGCTCCCCTTTACTGTCCCTTCCCCGCAG
CCAGCCCTGGACCCCAAAACTCCACATGGGTTCTGGAGATCTTCAAGCGGGGAACCTGGGGACAGAGGCCCAGGAACAGA
GGGTCATAGAAGAAAGCTCTTTAGACCAGGAGAAGATCCCAGAGGATAAGGACGAAGACCCTACTGAGGTTCCAACCCAG
ACACTGGAGCAGAACCTCAGACCCCCACTGTCAGAGTCTGCTGGTCTGACCCTGCAGCCTAAGCCAGTGGCCAGCCACCT
ATCACCACAGAACCTGGATGGGGATCGTTATAAACACTTGGCCCTGCAGGTGCTGTGCCTGGCCCAGAAACAGTATTCCC
TGCTGCAGGCAGCCAACCTCCTGACCCCTGACATGATTACTGAGTTCGAGACCATGCAGCAGCTGGTGCAAGAAGAGAAA
GCCGAGCCTGGAGACAAGACCTCCAGGACTCCTGGCCGGGCTGGGCGGGCCTCTCTGACCCAGGAGCTGTGTTCAGCCTC
AAAGTCTCCAGGGTACTGTGGCCCTGTGACCAAACAATGGCAAGAAGATTGAGTGGCCTCATGCACACTCTGGGGATCCC
ACCTGAGCCTGATTGCACCCCAGCCTCAGCATCCCGATAGCCCACAGAGAAGAAGAAGAGAAAG

Alignment

ORF - retro_itri_1104 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 90.72 %
• Parental protein coverage: 73.75 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  GVAMVMAVEDSMVQVMVRVRPPTPRELESQRWPVVQVVDERVLVFDPEEPDGSLKWGVTHDGPKKKGKGL
          GV.MVMAV.D.MVQV.VRVRPPT.RELESQRWPVVQVVDERVLVFDPEEPDG.LKWG.THDGPKKKGK.L
Retrocopy GVTMVMAVQDNMVQVVVRVRPPTSRELESQRWPVVQVVDERVLVFDPEEPDGGLKWGGTHDGPKKKGKDL

Parental  TFVFDRVFGEKATQQDVFQHTTSRILDSFLQGYNCSVFAYGATGAGKTHTMLGKEGDPGIMYLTTMELYK
          TFVFDRVFGEKATQQD.FQHTT.RILDSFLQGYNCSVFAYGATGAGKTHTMLGKEGDPGI.YLTTMELY.
Retrocopy TFVFDRVFGEKATQQDMFQHTTCRILDSFLQGYNCSVFAYGATGAGKTHTMLGKEGDPGIVYLTTMELYR

Parental  RFEAFQEEKQFEVLISYLEVYNEQIHDLLEPKGPLIIREDPDKGVMVQGLSFHQPASAEQLLKMLTRGNH
          RFEA.QEEKQFEVLISYLEVYNEQIHDLLEPKGPLIIREDPDKGV.VQGLSFHQPASAEQLLKMLTRGNH
Retrocopy RFEACQEEKQFEVLISYLEVYNEQIHDLLEPKGPLIIREDPDKGVVVQGLSFHQPASAEQLLKMLTRGNH

Parental  NRTQHPTDANATSSRSHAIFQIFVKQQDRVPGLTQALQVAKMSLIDLAGSERASSTHAKGERLREGANIN
          NRT.HPTDANATSSRSHAIFQIFVKQQDRVPGLTQALQVAKMSLIDLAGSER.SS..AKGERLREGANIN
Retrocopy NRTEHPTDANATSSRSHAIFQIFVKQQDRVPGLTQALQVAKMSLIDLAGSERSSSSGAKGERLREGANIN

Parental  RSLLALINVLNALVDAKGRKSHVPYRDSKLTRLLKDSIGGNCRTVMIAAISPSSLSYEDTYNTLKYADRA
          RSLLALINVLNALVDAKGRKSHVPYRDSKLTRLLKDSIGGNCRTVMIAAISPSSL.Y.DTYNTLKYADRA
Retrocopy RSLLALINVLNALVDAKGRKSHVPYRDSKLTRLLKDSIGGNCRTVMIAAISPSSLAYKDTYNTLKYADRA

Parental  KEIKLTLKSNVISLDSHISQYVTICQQLQAEVASLRKKLQVYEAGAQAPQQGLPQSSKLSPQQQHLSSSP
          KEI.LTLKSNV.SLD.HISQY.T.CQQLQAEVASLRKKLQ.YEAGAQAPQQGLPQ..KLSPQQQHL.SSP
Retrocopy KEIRLTLKSNVVSLDCHISQYATVCQQLQAEVASLRKKLQAYEAGAQAPQQGLPQPPKLSPQQQHLPSSP

Parental  LVSRPRSQPWTPELHVGSGDLQEGSLGTEAQEQRIIKESSSDQEQTPEDKDEDPTEVPTQTLEQNLTPPL
          L.S.PRSQPWTP.LH.GSGDLQ.G.LGTEAQEQR.I.ESS.DQE..PEDKDEDPTEVPTQTLEQNL.PPL
Retrocopy LLSLPRSQPWTPKLHMGSGDLQAGNLGTEAQEQRVIEESSLDQEKIPEDKDEDPTEVPTQTLEQNLRPPL

Parental  SESAGLTPQPKPVASHLSPQNLDGDRSKQLALQVLCLAQKQYSLLQAANLLTPDMITEFETLRQLVQEEK
          SESAGLT.QPKPVASHLSPQNLDGDR.K.LALQVLCLAQKQYSLLQAANLLTPDMITEFET..QLVQEEK
Retrocopy SESAGLTLQPKPVASHLSPQNLDGDRYKHLALQVLCLAQKQYSLLQAANLLTPDMITEFETMQQLVQEEK

Parental  AAPGDKTSRTPGLAGRAPLTQELCSASKSPRYCGPVTR-TMARRLSGLMHPLGIPSEPDCTLASASQQPT
          A.PGDKTSRTPG.AGRA.LTQELCSASKSP.YCGPVT..TMARRLSGLMH.LGIP.EPDCT.ASAS..PT
Retrocopy AEPGDKTSRTPGRAGRASLTQELCSASKSPGYCGPVTK<TMARRLSGLMHTLGIPPEPDCTPASASR*PT

Parental  EEKKKK
          E.KK.K
Retrocopy EKKKRK

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_1104 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_1104 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 2 parental genes, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Ictidomys tridecemlineatus	ENSSTOG00000007553	1 retrocopy	retro_itri_1104 ,
Ictidomys tridecemlineatus	ENSSTOG00000012710	1 retrocopy	retro_itri_40,