RetrogeneDB ID: retro_itri_1052

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393363.1:6143496..6145515(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSSTOG00000021156
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: KIF9
• Ensembl ID: ENSSTOG00000014845
• Aliases: None
• Description: kinesin family member 9 [Source:HGNC Symbol;Acc:16666]

Sequence

>retro_itri_1052
CGTGCTCTGCAGCAGGTTTTTAAGATGATCGAAGAGCGCCCCACACATGCCATCACTGTGCGTGTTTCCTACTTGGAAAT
CTATAATGAGAGCCTGTTTGATCTCCTGTCTACTCTGCCCTATGTTGGACCTTCAGTCACACCAATGACCATTGTGGAAA
ATCCTCAGGGGGTCTTCATTAAGGGCTTGTCAGTCCACCTCACAAGTCAGGAGGAGGATGCATTTAGTCTCCTTTTTGAG
GGAGAGACCAACAGGATTATAGCTTCCCACATGATGAACAAAAACTCATCCAGGTCACACTGCATTTTCACCATCTACAT
GGAGGCGCATTCCCGGACCTTATCAGATGAAAAGTATGTTACTTCCAAAATTAACTTGGTGGATCTGGCAGGCTCAGAGA
GGCTGGGGAAGTCTGGGTCTGAGGGTCGAGTTCTGAAGGAAGCCACCTACATCAACAAGTCGCTGTCTTTCCTGGAGCAA
GCCATCATTGTCCTTGGGGACCATAAGCGGGACCACATCCCTTTCCGACAGTGGAAGCTCACTCATGCCCTGAAGGACTC
CTTAGGGGGAAACTGCAACATGGTCCTTGTGACAAACATCTATGGAGAAGCCGCCCAGTTGGAAGAAACGTTATCCTTAC
TGCGATTTGCCAGCAGAATGAAGCTGGTCACCACTGAGCCTGCCATCAACGAAAAGTACAATGCTGAGCGAATGGTCAAG
AACCTGGAGAAGGAGCTAGTATTGCTCAAGCAGGAGCTAGCCATCCATGACAGCCTGGCCAACCGCAACATTGTGACCTA
TGACCCCATGGATGAAATCCAGATTGCTGAGATCAACTCCCAGGTGCGGAGGTACCTGGAAGGGACACTGGACGAGATTG
ACATAATCAACCTCAGACAGATTCAGGAGGTATTCAACCAATTCTGGGTGGTTCTGAGCCAACAAGAACAGGAAGTGGAG
GCGGCCTTACGTAGGAAGTACACTCTTATAGACAAGAATGACTTTGCAACAATTTCTGCTGTCCAGAAGGCAGGGATTAT
TGATGTTAATGGCCACCTAGTAGGTGAGCCTGATGGACAAGGCTTTGGACTTGGGGTTGCCCCTTTCTCTACCAAACCTG
CGAAGAAATCCAAGTCCAAGAAGACAGTCAAAGATCCGCCCAGCTCATCAGCAAGAAAGGAAGGTGCTAGCAGCCCTGTG
AGTGGCAAGGACCTAGATATGATTTCTACCTCCAAGACCCAGCTAGTCCCATCCTCTAAGGATGGGGATGTTAAAGACGT
GCTTTCTCGGGATCGGGAAACTTCCAGCATTGAGCCCCTTCCCTCAGACTCCCCGAAGGAAGAATCACGCCCACTCAGGC
CTACCACCCCACCCTCCAAACTGATGGCCTTTGAGGACTTTAAGAATGAGCGAGGAAGTGAGATCAACCGCATCTTCAAA
GAAAATAAGTCCATCTTGAATGAGCGGAGGAAAAGGGCCAGCGAGACCACACAGCACATCAATGTCATCAAGCGGGAGAT
TGACGTGACCAAAGAAGCGCTAAACTCCCAGAAGTCACTACGGGAGAAGCAAGGTGAGTATGAGAACAAGGGGCTGATGA
TCATTGATGAAGAGGAATTCTTGCTGATCCTGAAGCTCAAAGACCTCAAGAAGCAGTATCGAAGCGAGTACCAGGATCTG
CGTGACCTCAGGGCTGAGATTCAGTACTGCCAACACCTGGTGGACCAGTGTCGCCACCGCCTGCTCATGGAATTTGATAT
CTGGTACAATGAGTCCTTTGTCATCCCTGAGGATATGCAGGTAGCACTGAAGCTGGGCAGCAGTATCGGGCCAGGCATGG
TGCCTGTCAGCAGGATCGTTTCTCTGGGAGAAGATGACCAGGACAACTTTGCTCAGCTTCAGCAGACAGTGCTACCCGAA
GGACCTGATGCCATCTCCTTCTACAATGCCAAAATCAAGACAGAACAGAAGCATAATTACTTGAAAACCATAATGGGCCT
CCAGCAGACACATTAAAAA

Alignment

ORF - retro_itri_1052 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 98.37 %
• Parental protein coverage: 85.19 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  RALQQVFKMIEERPTHAITVRVSYLEIYNESLFDLLSTLPYVGPSVTPMTIVENPQGVFIKGLSVHLTSQ
          RALQQVFKMIEERPTHAITVRVSYLEIYNESLFDLLSTLPYVGPSVTPMTIVENPQGVFIKGLSVHLTSQ
Retrocopy RALQQVFKMIEERPTHAITVRVSYLEIYNESLFDLLSTLPYVGPSVTPMTIVENPQGVFIKGLSVHLTSQ

Parental  EEDAFSLLFEGETNRIIASHTMNKNSSRSHCIFTIYMEAHSRTLSDEKYVTSKINLVDLAGSERLGKSGS
          EEDAFSLLFEGETNRIIASH.MNKNSSRSHCIFTIYMEAHSRTLSDEKYVTSKINLVDLAGSERLGKSGS
Retrocopy EEDAFSLLFEGETNRIIASHMMNKNSSRSHCIFTIYMEAHSRTLSDEKYVTSKINLVDLAGSERLGKSGS

Parental  EGRVLKEATYINKSLSFLEQAIIALGDHKRDHIPFRQCKLTHALKDSLGGNCNMVLVTNIYGEAAQLEET
          EGRVLKEATYINKSLSFLEQAII.LGDHKRDHIPFRQ.KLTHALKDSLGGNCNMVLVTNIYGEAAQLEET
Retrocopy EGRVLKEATYINKSLSFLEQAIIVLGDHKRDHIPFRQWKLTHALKDSLGGNCNMVLVTNIYGEAAQLEET

Parental  LSSLRFASRMKLVTTEPAINEKYNAERMVKNLEKELVLLKQELAIHDSLANRNIVTYDPMDEIQIAEINS
          LS.LRFASRMKLVTTEPAINEKYNAERMVKNLEKELVLLKQELAIHDSLANRNIVTYDPMDEIQIAEINS
Retrocopy LSLLRFASRMKLVTTEPAINEKYNAERMVKNLEKELVLLKQELAIHDSLANRNIVTYDPMDEIQIAEINS

Parental  QVRRYLEGTLDEIDIINLRQIQEVFNQFRVVLSQQEQEVEAALRRKYTLIDKNDFATISAVQKAGIIDVN
          QVRRYLEGTLDEIDIINLRQIQEVFNQF.VVLSQQEQEVEAALRRKYTLIDKNDFATISAVQKAGIIDVN
Retrocopy QVRRYLEGTLDEIDIINLRQIQEVFNQFWVVLSQQEQEVEAALRRKYTLIDKNDFATISAVQKAGIIDVN

Parental  GHLVGEPDGQGFGLGVAPFSTKPGKKSKSKKTVKDPPSSSARKEGASSPVSGKDLDMISTSKTQLVPSSK
          GHLVGEPDGQGFGLGVAPFSTKP.KKSKSKKTVKDPPSSSARKEGASSPVSGKDLDMISTSKTQLVPSSK
Retrocopy GHLVGEPDGQGFGLGVAPFSTKPAKKSKSKKTVKDPPSSSARKEGASSPVSGKDLDMISTSKTQLVPSSK

Parental  DGDVKDVLSRDRETSSIEPLPSDSPKEESRPLRPTTPPSKLMAFEDFKNERGSEINRIFKENKSILNERR
          DGDVKDVLSRDRETSSIEPLPSDSPKEESRPLRPTTPPSKLMAFEDFKNERGSEINRIFKENKSILNERR
Retrocopy DGDVKDVLSRDRETSSIEPLPSDSPKEESRPLRPTTPPSKLMAFEDFKNERGSEINRIFKENKSILNERR

Parental  KRASETTQRINVIKREIDVTKEALNFQKSLREKQGEYENKGLMIIDEEEFLLILKLKDLKKQYRSEYQDL
          KRASETTQ.INVIKREIDVTKEALN.QKSLREKQGEYENKGLMIIDEEEFLLILKLKDLKKQYRSEYQDL
Retrocopy KRASETTQHINVIKREIDVTKEALNSQKSLREKQGEYENKGLMIIDEEEFLLILKLKDLKKQYRSEYQDL

Parental  RDLRAEIQYCQHLVDQCRHRLLMEFDIWYNESFVIPEDMQVALKLGSSIRPGMVPVSRIVSLGEDDQDKF
          RDLRAEIQYCQHLVDQCRHRLLMEFDIWYNESFVIPEDMQVALKLGSSI.PGMVPVSRIVSLGEDDQD.F
Retrocopy RDLRAEIQYCQHLVDQCRHRLLMEFDIWYNESFVIPEDMQVALKLGSSIGPGMVPVSRIVSLGEDDQDNF

Parental  AQLQQTVLPEGPDAISFYNAKIKTEQKHNYLKTIMGLQQTHKK
          AQLQQTVLPEGPDAISFYNAKIKTEQKHNYLKTIMGLQQTH.K
Retrocopy AQLQQTVLPEGPDAISFYNAKIKTEQKHNYLKTIMGLQQTH*K

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_1052 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_1052 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 1 parental gene, and 1 retrocopy.

Species	Parental gene accession	Retrocopies number
Ictidomys tridecemlineatus	ENSSTOG00000014845	1 retrocopy	retro_itri_1052 ,