RetrogeneDB ID: retro_itri_56

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393281.1:13909776..13910445(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSSTOG00000019474
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSSTOG00000020509
• Aliases: None
• Description: None

Sequence

>retro_itri_56
ATGGCATTTGTGAAGAGTGGATGGTTGCTGCGACAGAGTACTATTTTGAAGCGCTGGAAGAAGAATTGGTTTGACCTGTG
GTCAGATGGTCACCTGATCTATTATGATGACCAAACTCGGCAGAGTATTGAGGATAAGGTCCATATGCCGGTAGATTGCA
TCAATATCCGCACAGGGCATGAGTGTCGGGATATTCAGCCTCCAGATGGGAAGCCAAAAGACTGTCTGCTGCAGATTGTT
TGCCGAGATGGGAAAACTATCAGTCTTTGTGCAGAAAGCACAGATGATTGTTTGGCCTGGAAATTTGCACTGGAAGATTC
TAGAACAAACACAGCTTATGTTGGCTCACCAGTCCTTTCCGAGGAGACAGTTGTGGCTGCTTCACCCCCTCCATACACAG
CCTATGCTGCACCAACTCCTGAGCAGGTATATGGCTATGGTCCGTACGGTGGTGCATACCCAGCAGGAACTCAGGTTGTC
TATGCTGCCAATGGCCAGGCGTATGCTGTGCCCTACCAGTACCCATATGCAGGACTTTATGGACAACAGCCTGCCAACCA
AGTCATCATTCGTGAACGGTATCATGACAATGACAGTGACCTGGCACTAGGCATGTTGGCTGGAGCGGCCACAGGCATGG
CCTTAGGGTCTCTGTTTTGGGTTTTCTAG

Alignment

ORF - retro_itri_56 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 86.1 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MAFVKSGWLLRQSTILKRWKKNWFDLWSDGHLIYYDDQTRQSIEDKVHMPVDCINIRTGHECRDIQPPDG
          MAFVKSGWLLRQSTILKRWKKNWFDLWSDGHLIYYDDQTRQSIEDKVHMPVDCINIRTGHECRDIQPPDG
Retrocopy MAFVKSGWLLRQSTILKRWKKNWFDLWSDGHLIYYDDQTRQSIEDKVHMPVDCINIRTGHECRDIQPPDG

Parental  KPKDCLLQIVCRDGKTISLCAESTDDCLAWKFALQDSRTNTAYVGSPVLSEETVVAASPPPYTAYAAPTP
          KPKDCLLQIVCRDGKTISLCAESTDDCLAWKFAL.DSRTNTAYVGSPVLSEETVVAASPPPYTAYAAPTP
Retrocopy KPKDCLLQIVCRDGKTISLCAESTDDCLAWKFALEDSRTNTAYVGSPVLSEETVVAASPPPYTAYAAPTP

Parental  E-VYNFLMYIYEYTTVNLIIHYWVLNSGALVPVEYRFSRLYGQQPANQVIIRERYHDNDSDLALGMLAGA
          E.VY....Y...Y........Y........VP..Y....LYGQQPANQVIIRERYHDNDSDLALGMLAGA
Retrocopy EQVYGYGPYGGAYPAGTQVV-YAANGQAYAVPYQYPYAGLYGQQPANQVIIRERYHDNDSDLALGMLAGA

Parental  ATGMALGSLFWVF
          ATGMALGSLFWVF
Retrocopy ATGMALGSLFWVF

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_56 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_56 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.

---

Parental genes homology:

Parental genes homology involve 12 parental genes, and 15 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000000941	2 retrocopies	retro_btau_1134, retro_btau_1635,
Cavia porcellus	ENSCPOG00000026329	1 retrocopy	retro_cpor_985,
Equus caballus	ENSECAG00000017331	1 retrocopy	retro_ecab_1069,
Felis catus	ENSFCAG00000027063	1 retrocopy	retro_fcat_213,
Homo sapiens	ENSG00000115762	1 retrocopy	retro_hsap_1890,
Meleagris gallopavo	ENSMGAG00000001052	1 retrocopy	retro_mgal_17,
Monodelphis domestica	ENSMODG00000018634	1 retrocopy	retro_mdom_720,
Nomascus leucogenys	ENSNLEG00000010698	2 retrocopies	retro_nleu_1471, retro_nleu_2016,
Oryctolagus cuniculus	ENSOCUG00000024282	1 retrocopy	retro_ocun_654,
Otolemur garnettii	ENSOGAG00000028408	2 retrocopies	retro_ogar_2771, retro_ogar_703,
Pongo abelii	ENSPPYG00000012740	1 retrocopy	retro_pabe_1570,
Ictidomys tridecemlineatus	ENSSTOG00000020509	1 retrocopy	retro_itri_56 ,