RetrogeneDB ID: retro_itri_1862

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH394246.1:38962..39820(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: KLF4
• Ensembl ID: ENSSTOG00000022002
• Aliases: None
• Description: Kruppel-like factor 4 (gut) [Source:HGNC Symbol;Acc:6348]

Sequence

>retro_itri_1862
GCGGAGCTCCTGCGGCCCGAATTGGACCCCGTGTACATTCCGCCGCAGCAACCGCAGCCGCCACGTGGCGGGCTGATGGG
CAAGTTTGTGCTGAAGGCATCGTTGAGTGCCCCTGGCAGCGAGTACGGCAGCCCGTCGGTCATCAGTGTTAGCAAAGGCA
GCCCGGACGGCAGCCACCCGGTGGTGGTAGCGCCCTACAGCAGCGGGCCGCCTCGCATGTGCCCCAAGATCAAGCAGGAG
GCAGTTTCTTCGTGCACGGTCGGTCGACCCCTAGAGGCCCACTTGGGCGCTGGACCCCCGCTCAGCAATGGGCACCGGCC
TAGCGCGCATGACTTCTCCCTGGGGCAGCAGCTCCCCAGCAGGACTACCCCGACCCTGGGTCCTGAAGAACTGCCGAGCA
ACCGGGACTGTCACTCTGTCTTGCCGCTTCCCCCAGGATTCCATCCCCATCCGGGACCGAACTAACCACCCTTCCTGTCT
GACCAGATGTAGCCACAGGTCCCACCACTCCACTACCAAGAGCTCATGCCACCTGGTTCCTGCCTGCCAGAGGAACCCAA
GCCAAAGAGGGGAAGAAGGTCTTGGCCCCAGAAAAGGACTGCCACTCACACTTGCGATTATGCCGGTTGCGGCAAAACCT
ACACAAAGAGTTCTCATCTCAAGGCACACCTGCGAACCCACACAGGTGAGAAACCTTACCACTGTGACTGGGATGGCTGC
GGGTGGAAATTTGCCCGCTCTGATGAACTGACCAGGCACTACCACAAACACACCGGGCACCGCCCATTCCAGTGCCAGAA
GTGCGACCGGGCCTTTTCCAGGTGGGACCACCTGGCCTTACACATGAAGAGGCACTTT

Alignment

ORF - retro_itri_1862 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 96.85 %
• Parental protein coverage: 58.97 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  AELLRPELDPVYIPPQQPQPPGGGLMGKFVLKASLSAPGSEYGSPSVISVSKGSPDGSHPVVVAPYSSGP
          AELLRPELDPVYIPPQQPQPP.GGLMGKFVLKASLSAPGSEYGSPSVISVSKGSPDGSHPVVVAPYSSGP
Retrocopy AELLRPELDPVYIPPQQPQPPRGGLMGKFVLKASLSAPGSEYGSPSVISVSKGSPDGSHPVVVAPYSSGP

Parental  PRMCPKIKQEAVSSCTVGRPLEAHLGAGPPLSNGHRPSAHDFSLGRQLPSRTTPTLGPEELLSNRDCHSA
          PRMCPKIKQEAVSSCTVGRPLEAHLGAGPPLSNGHRPSAHDFSLG.QLPSRTTPTLGPEEL.SNRDCHS.
Retrocopy PRMCPKIKQEAVSSCTVGRPLEAHLGAGPPLSNGHRPSAHDFSLGQQLPSRTTPTLGPEELPSNRDCHSV

Parental  LPLPPGFHPHPGPNYPPFLSDQMQPQVPPLHYQELMPPGSCLPEEPKPKRGRRSWPRKRTATHTCDYAGC
          LPLPPGFHPHPGPN.PPFLSDQM.PQVPPLHYQELMPPGSCLPEEPKPKRGRRSWP.KRTATHTCDYAGC
Retrocopy LPLPPGFHPHPGPN*PPFLSDQM*PQVPPLHYQELMPPGSCLPEEPKPKRGRRSWPQKRTATHTCDYAGC

Parental  GKTYTKSSHLKAHLRTHTGEKPYHCDWDGCGWKFARSDELTRHYRKHTGHRPFQCQKCDRAFSRSDHLAL
          GKTYTKSSHLKAHLRTHTGEKPYHCDWDGCGWKFARSDELTRHY.KHTGHRPFQCQKCDRAFSR.DHLAL
Retrocopy GKTYTKSSHLKAHLRTHTGEKPYHCDWDGCGWKFARSDELTRHYHKHTGHRPFQCQKCDRAFSRWDHLAL

Parental  HMKRHF
          HMKRHF
Retrocopy HMKRHF

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_1862 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_1862 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 5 parental genes, and 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000020355	1 retrocopy	retro_btau_521,
Pongo abelii	ENSPPYG00000019478	7 retrocopies	retro_pabe_1836, retro_pabe_2020, retro_pabe_2022, retro_pabe_2024, retro_pabe_2027, retro_pabe_2037, retro_pabe_3579,
Rattus norvegicus	ENSRNOG00000016299	1 retrocopy	retro_rnor_2164,
Ictidomys tridecemlineatus	ENSSTOG00000015926	1 retrocopy	retro_itri_569,
Ictidomys tridecemlineatus	ENSSTOG00000022002	1 retrocopy	retro_itri_1862 ,