RetrogeneDB ID: retro_itri_1620

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393578.1:1167242..1168350(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSSTOG00000023180
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: TRMT6
• Ensembl ID: ENSSTOG00000006863
• Aliases: None
• Description: tRNA methyltransferase 6 homolog (S. cerevisiae) [Source:HGNC Symbol;Acc:20900]

Sequence

>retro_itri_1620
TTAATTGAAAATAGTACAACATTCCGAGACAAGACAGAATTTGCTCAAGATAAATATATAAAAAAGAAGAAAAAGAAATA
TGAAGCTGTCATAACTATTTTGAAGCCATCAACCAGTATTCTTTCAATTATGTATTATGCAAGAGAACCTGGAAAAATTA
ACCATATGAGATATGATACACTAGCCCAGATGCTGACATTGGGAAATATCCATGCTGGCAATAAAATGATTGTAATGGAA
ACATGTTCAGGCTTGGTGCTGGGTGCAATGATGGAACGAATGGGAGGTTTTGGCTCCATTATTCAGCTCTACCCTGGAGA
CGGACCTGTTCGGGTAGCAACAGCGTGTTTTGGATTTCCCAAATCTTTTCTCAGTGGTCTTTATGAATTTCCCCCTCAAC
AAAGTGGATAGTCTCCTAAATGGAACATTTTCTGCTGAGATATTATACGCAGAGCCAAAAGACAGTGCATCAGTTGAAGA
AAGTAATGGTGCACTTGAGGAAAAGCAGGCTTCTAAACCAGACAATGAAGACAGCATGGCAGAGGCCCCAGAGAGCAATC
ACCCAGAACAAGAATCAATGGAAGTTGTTCCTCAAGATCCAGAATATAAGGAGCCTAAAGATAGAGGAAGCAAAAAAGAT
TATATTCAGGAAAAGCAAAGGAGACAAGAAGAGCAGAGGAAGAGACACTTAGATGCTGCTGCTCTACTGAGTGAAAGGAA
CGCAGATGGTTTAATTGTAGCCAGTCGTTTTCATCCCACTCCATTGCTCCTGTCTTTGTTGGACTTTGTGGCCCCTTCAA
GGCCATTTGTGGTCTACTGTCAGTATAAAGAGCCTTTGTTGGAATGCTACATAAAACTTTGTGAGGGGGGAGGAGTCATC
AACCTCAGGCTGTCTGAAACCTGGCTCAGAAATTATCAGGTTTTGCCAGATCGAAGTCATCCCAAGCTGCTGATGAGTGG
AGGCAGGGGGTACCTTCTGTCAGGCTTCACTGTTGTCTTGGACAATCTTCGAGCAGACACCAGCCTCAAGTCCAGCGTGA
GCACTTTAGAATCACACAAGACTGAAGAACCAGCAGCTAAAAGGCAGAAATGTCCAGAATCTGGCTCT

Alignment

ORF - retro_itri_1620 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 97.57 %
• Parental protein coverage: 74.4 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  LIENSTTFRDKTEFAQDKYIKKKKKKYEAVITILKPSTRILSIMYYAREPGKINHMRYDTLAQMLTLGNI
          LIENSTTFRDKTEFAQDKYIKKKKKKYEAVITILKPST.ILSIMYYAREPGKINHMRYDTLAQMLTLGNI
Retrocopy LIENSTTFRDKTEFAQDKYIKKKKKKYEAVITILKPSTSILSIMYYAREPGKINHMRYDTLAQMLTLGNI

Parental  RAGNKMIVMETCSGLVLGAMMERMGGFGSIIQLYPGDGPVRVATACFGFPKSFLSGLYE-FPLNKVDSLL
          .AGNKMIVMETCSGLVLGAMMERMGGFGSIIQLYPGDGPVRVATACFGFPKSFLSGLYE.FPLNKVDSLL
Retrocopy HAGNKMIVMETCSGLVLGAMMERMGGFGSIIQLYPGDGPVRVATACFGFPKSFLSGLYE>FPLNKVDSLL

Parental  NGTFSAEILYAEPKDSASVEESNGALEEKQASKPDNEDSMAEAPESNHPEQESMEVVPQDPEYKEPKDRR
          NGTFSAEILYAEPKDSASVEESNGALEEKQASKPDNEDSMAEAPESNHPEQESMEVVPQDPEYKEPKDR.
Retrocopy NGTFSAEILYAEPKDSASVEESNGALEEKQASKPDNEDSMAEAPESNHPEQESMEVVPQDPEYKEPKDRG

Parental  SKKDYIQEKQRRQEEQRKRHLDAAALLSERNADGLIVASRFHPTPLLLSLLDFVAPSRPFVVYCQYKEPL
          SKKDYIQEKQRRQEEQRKRHLDAAALLSERNADGLIVASRFHPTPLLLSLLDFVAPSRPFVVYCQYKEPL
Retrocopy SKKDYIQEKQRRQEEQRKRHLDAAALLSERNADGLIVASRFHPTPLLLSLLDFVAPSRPFVVYCQYKEPL

Parental  LECYTKLRERGGVINLRLSETWLRNYQVLPDRSHPKLLMSGGGGYLLSGFTVVLDNLRADTSLKSSASTL
          LECY.KL.E.GGVINLRLSETWLRNYQVLPDRSHPKLLMSGG.GYLLSGFTVVLDNLRADTSLKSS.STL
Retrocopy LECYIKLCEGGGVINLRLSETWLRNYQVLPDRSHPKLLMSGGRGYLLSGFTVVLDNLRADTSLKSSVSTL

Parental  ESHKTEEPAAKRQKCPESGS
          ESHKTEEPAAKRQKCPESGS
Retrocopy ESHKTEEPAAKRQKCPESGS

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_1620 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_1620 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 2 parental genes, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Rattus norvegicus	ENSRNOG00000021270	1 retrocopy	retro_rnor_656,
Ictidomys tridecemlineatus	ENSSTOG00000006863	1 retrocopy	retro_itri_1620 ,