RetrogeneDB ID: retro_itri_77

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393592.1:759273..760581(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSSTOG00000022342
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSSTOG00000014763
• Aliases: None
• Description: None

Sequence

>retro_itri_77
ATGGAACCTGAAGACTTTGATTCTGAAGACAAAGAGGTATTAAACTGGGACATTAATGACATGAAACTGCCACAGAATGT
GAAAAAGACTGACTGGTTCCAGGAGTGGCCAGATTCCTATGTGAAGCACATCTACAGCTCAGAGGACAGGAATGCGCAGC
GACACCTGAGCAGCTGGGCCATGCGCAACACGAACAACCACAACTCTCGCATCCTCAAGAAGTCCTGTCTGGGTGTGGTG
GTGTGCGGCCACAACTGCTCTACCAAGGAGGGGCGCAAGGTCTACCTGAGACCTGCAATCTGTGACAAAGCCTGGCAGAA
GCAGCAGAAGAAAAGTTGTCCCAACTGTAATGGGCCTTTGAAGCTGATTCCTTGCCAAGGCCATGGGGGCTTCCCCGTCA
CCAACTTCTGGAGACACGATGGACACTTCATATTCTTCCAGTCAAAGGGAGAGCATGATCATCCAAAGCCGGAAACCAAG
TTAGAAGCTGAGGCAAGAAGAGCAATGAAGAAAGTGCATGGGGCACCTGCCTCTGTCTCCCTAAAGCTGAAGGGGAACCC
AGGATCCAAGTCTCTTCCAGGTGAAACACAAAGTCAGGGAAGTTTACCTTTAACTTGGTCATTCCAGGAAGGTGTCCAAT
TGCCTGGCAGTTACAGTGGACATTTAATAGCTAACACTCCCCAGCCGAATTCACTGAATGATTGCTTATCCTTCTCCAAG
AGTTATGGTTCAGGGGGAACCACTGATCTGGCAGACCCGGCTTCCACCTTAGACCCCACTAAGCTGTATGAAAAATGCAG
ATTTTCCAGTAATAGGATCTACAATAGTGGAGACCTGTTTCAGCCTTCTGCCTCTGGAGTCTACTCAGATTATGACAATC
TGCAAGCATGGAATAAAAACGCTGCTTTGGGGAGAAGCCCTCTCAATGACAACTATTGTCCCAATTATCCTTTTCCTCTG
ACCGGCTGGCCTTGTGACTTCTTTCCTTCCCAGAATTCTCTGGAGAACTTTCCCCAGCAGATTCCCCTGGAACCACCTGC
TGCCAAAACTAGCTGCCACCCATTATGGCCAAATCCAGGGGGCGAGCTTTATGAAGAGAAAGTGCCTGTGGATTTCAACA
GCTACGTTCCTTCTCTCGCTTACCATCCACCACAGGAAGACCCCTTTCTGTTCACCTACACCCCCCATCCTCACCAGCAA
TGCACCCTGCCAGGCAAGACCACCAAGTGGGATTTTGAGGAAGAAATGACATATATGGGTTTGGATCATTGCAACAATGA
AATGCTTCTAAACCTCTGTCCTTTAAGA

Alignment

ORF - retro_itri_77 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 90.83 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MEPEDFDSEDKEVLNWDINDMKLPQNVKKTDWFQEWPDSYVKHIYSSEDRNAQRHLSSWAMRNTNNHNSR
          MEPEDFDSEDKEVLNWDINDMKLPQNVKKTDWFQEWPDSYVKHIYSSEDRNAQRHLSSWAMRNTNNHNSR
Retrocopy MEPEDFDSEDKEVLNWDINDMKLPQNVKKTDWFQEWPDSYVKHIYSSEDRNAQRHLSSWAMRNTNNHNSR

Parental  ILKKSCLGVVVCGHNCSTKEGRKVYLRPAICDKARQKQQKKSCPNCNGPLKLIPCRGHGGFPVTNFWRHD
          ILKKSCLGVVVCGHNCSTKEGRKVYLRPAICDKA.QKQQKKSCPNCNGPLKLIPC.GHGGFPVTNFWRHD
Retrocopy ILKKSCLGVVVCGHNCSTKEGRKVYLRPAICDKAWQKQQKKSCPNCNGPLKLIPCQGHGGFPVTNFWRHD

Parental  SLVLFFPSKFPYASRKVEDRREGERRRERQSIRFMPGCVSIERKEIQLLLSLPGETQSQGSLPLTWSFQE
          ....FF.SK......K.E...E.E.RR........P..VS...K......SLPGETQSQGSLPLTWSFQE
Retrocopy GHFIFFQSKGEHDHPKPETKLEAEARRAMKKVHGAPASVSLKLKGNPGSKSLPGETQSQGSLPLTWSFQE

Parental  GVQLPGSYSGHLIANTPQPNSLNDCLSFSKSYGSGGTTDLADPASTLDPTKLYEKCRFSSNRIYNSGDLF
          GVQLPGSYSGHLIANTPQPNSLNDCLSFSKSYGSGGTTDLADPASTLDPTKLYEKCRFSSNRIYNSGDLF
Retrocopy GVQLPGSYSGHLIANTPQPNSLNDCLSFSKSYGSGGTTDLADPASTLDPTKLYEKCRFSSNRIYNSGDLF

Parental  QPSASGVYSDYDNLQAWNKNAALGRSPLNDNYCPNYPFPLTGWPCDFFPSQNSLENFPQQIPLEPPAAKT
          QPSASGVYSDYDNLQAWNKNAALGRSPLNDNYCPNYPFPLTGWPCDFFPSQNSLENFPQQIPLEPPAAKT
Retrocopy QPSASGVYSDYDNLQAWNKNAALGRSPLNDNYCPNYPFPLTGWPCDFFPSQNSLENFPQQIPLEPPAAKT

Parental  SCHPLWPNPGGELYEEKVPVDFNSYVPSLAYHPPQEDPFLFTYNPHPHQQCTLPGKSTKWDFEEEMTYMG
          SCHPLWPNPGGELYEEKVPVDFNSYVPSLAYHPPQEDPFLFTY.PHPHQQCTLPGK.TKWDFEEEMTYMG
Retrocopy SCHPLWPNPGGELYEEKVPVDFNSYVPSLAYHPPQEDPFLFTYTPHPHQQCTLPGKTTKWDFEEEMTYMG

Parental  LDHCNNEMLLNLCPLR
          LDHCNNEMLLNLCPLR
Retrocopy LDHCNNEMLLNLCPLR

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_77 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_77 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 3 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000002273	1 retrocopy	retro_cfam_466,
Rattus norvegicus	ENSRNOG00000007932	1 retrocopy	retro_rnor_2476,
Ictidomys tridecemlineatus	ENSSTOG00000014763	1 retrocopy	retro_itri_77 ,