RetrogeneDB ID: retro_itri_1889

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH394912.1:12190..12635(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: KCTD5
• Ensembl ID: ENSSTOG00000006647
• Aliases: None
• Description: potassium channel tetramerization domain containing 5 [Source:HGNC Symbol;Acc:21423]

Sequence

>retro_itri_1889
GAAAGGGATGCCTATTTAATTGACAGGATCCCAGGGACCTTGGAGCTGTGTTGAACTCCTTGAGACATGGGAAGCTGGTC
CTTAACAAAGACCTCGCTGAGGAAGAAGTGTGGGAAGAAGCAGAATTTTAAAATATCACCTCACTCACAAAACTTGTAAA
GGACAAAATTAGAGAAGGAGACAGCAAAACATCACAGGTGCCTGTGAAGCATGTATACCCTGTGTTCAGTGTCAGGAGGA
GGGGCTCACACAGATGGTGTCCACCATGCCTGATGGCTGGAAATTTGAGCAGCTGGTCAGAATTGGCTCCTCTTACCACT
ATGAGAATGAAGACCAGGCCGAGCTCTTCTATGTGGTTTCCAAGGAGCTGCCCAACACCCCATATGGCACAACCAGTGAG
CTCAGCGAGGAGGCCAAGATTTTGCAAGAACGGGGCTCAAGGATG

Alignment

ORF - retro_itri_1889 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 81.46 %
• Parental protein coverage: 99.33 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  ETGAYLIDR-DPTYFGPVLNYLRHGKLVINKDLAEEGVLEEAEFYNITSLIKLVKDKIRERDSKTSQVPV
          E..AYLIDR.DP...G.VLN.LRHGKLV.NKDLAEE.V.EEAEF.NITSL.KLVKDKIRE.DSKTSQVPV
Retrocopy ERDAYLIDR<DPRDLGAVLNSLRHGKLVLNKDLAEEEVWEEAEF*NITSLTKLVKDKIREGDSKTSQVPV

Parental  KHVYRV-LQCQEEELTQMVSTMSDGWKFEQLVSIGSSYNYGNEDQAEFLCVVSKELHNTPYGTTSEPSEK
          KHVY.V..QCQEE.LTQMVSTM.DGWKFEQLV.IGSSY.Y.NEDQAE...VVSKEL.NTPYGTTSE.SE.
Retrocopy KHVYPV<VQCQEEGLTQMVSTMPDGWKFEQLVRIGSSYHYENEDQAELFYVVSKELPNTPYGTTSELSEE

Parental  AKILQERGSRM
          AKILQERGSRM
Retrocopy AKILQERGSRM

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_1889 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_1889 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 7 parental genes, and 14 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000019357	1 retrocopy	retro_cfam_433,
Homo sapiens	ENSG00000167977	1 retrocopy	retro_hsap_2224,
Gorilla gorilla	ENSGGOG00000010496	1 retrocopy	retro_ggor_1752,
Monodelphis domestica	ENSMODG00000016596	1 retrocopy	retro_mdom_506,
Sarcophilus harrisii	ENSSHAG00000006867	1 retrocopy	retro_shar_158,
Ictidomys tridecemlineatus	ENSSTOG00000006647	8 retrocopies	retro_itri_1562, retro_itri_1690, retro_itri_1692, retro_itri_1761, retro_itri_1779, retro_itri_1844, retro_itri_1889 , retro_itri_950,
Tursiops truncatus	ENSTTRG00000008237	1 retrocopy	retro_ttru_1510,