RetrogeneDB ID: retro_sara_419

Retrocopy location

• Organism: Shrew (Sorex araneus)
• Coordinates: scaffold_197796:1180..2050(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: IK
• Ensembl ID: ENSSARG00000007388
• Aliases: None
• Description: IK cytokine, down-regulator of HLA II [Source:HGNC Symbol;Acc:5958]

Sequence

>retro_sara_419
GAGCGAGATAGTAAGCCGTTTTCCAATCCTTTGGCCCCAGATGGCCATGATGTGGACGATCCTCACTCCTTCCACCAATC
TAAGCTCACCAATGAAGATTTCAGAAAACTTCTCATGACCCCAAGGGCTGCACCTACCTCTGCACCACCCTCTAAATCGA
GTCACCGTGAGATGCCAAGGGAGTATAATGAGGATGAGGATCCAGCTGCACAGAGGAGAAAAAAGAAAAGTTATTATGCA
AAACTTCACCAGCAGGAAATTGAGAGAGAGCGAGAACTTGGCAGAGAAATACTGGGACCGGGCCAAGGAACGAAGAGATG
ATGTGAACAAAGATTATGAGGAAACTGAGCTGATCAGCACCACAGCAAACTACAGGCCGTGGGCCCCACTGCTGAGGCAG
ACAAATCAGCTGCAGAGAAAAGACAGTTGATCCAGGAGTCCAAGTTCTTAGGTGGTGACATGGAACATACCCATTTGGTG
AAAGGCTTGGATTTTGCTCTGCTTCAGAAGGTACGAGCTGAGATTGCCAGCAAGGAGAAAGAGGAGGAAGAACTGATGGA
AAAGCCCCAGAAGGAAACCAAGAGAGATGAGGACCCTGAAAACAAAATTGAATTTAAAATTCATTTAGGTCGCAATGTTT
ACCGTATGCTCTTCAAGAGCAAAGCGTACGAATGGAATGAGCTGTTCCTGCCGGGCCGCATGGCCTATGTGGTGGACCTG
GATGATGAGTATGCGGACACGGACATCCCCATCACTCTTATCCGAAGCAAGGCGGACTGCCCCACCATGGAGGCCCAGAC
CACACTGACAACAAGTGACATTGTCATCAGCAAGCTCACACAGATTCTTTCCTACTTGAGGCAGGGTACC

Alignment

ORF - retro_sara_419 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 93.88 %
• Parental protein coverage: 96.37 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  ERGSREPFSNPLAPDGHDVDDPHSFHQSKLTNEDFRKLLMTPRAAPTSAPPSKSRHHEMPREYNEDEDPA
          ER.S..PFSNPLAPDGHDVDDPHSFHQSKLTNEDFRKLLMTPRAAPTSAPPSKS.H.EMPREYNEDEDPA
Retrocopy ERDSK-PFSNPLAPDGHDVDDPHSFHQSKLTNEDFRKLLMTPRAAPTSAPPSKSSHREMPREYNEDEDPA

Parental  ARRRKKKSYYAKLRQQEIEREREL-AEKYRDRAKERRDGVNKDYEETELISTTANYR-AVGPTAEADKSA
          A.RRKKKSYYAKL.QQEIEREREL.AEKY.DRAKERRD.VNKDYEETELISTTANYR.AVGPTAEADKSA
Retrocopy AQRRKKKSYYAKLHQQEIEREREL>AEKYWDRAKERRDDVNKDYEETELISTTANYR<AVGPTAEADKSA

Parental  AEKRRQLIQESKFLGGDMEHTHLVKGLDFALLQKVRAEIASKEKEEEELMEKPQKETKKDEDPENKIEFK
          AEK.RQLIQESKFLGGDMEHTHLVKGLDFALLQKVRAEIASKEKEEEELMEKPQKETK.DEDPENKIEFK
Retrocopy AEK-RQLIQESKFLGGDMEHTHLVKGLDFALLQKVRAEIASKEKEEEELMEKPQKETKRDEDPENKIEFK

Parental  TRLGRNVYRMLFKSKAYERNELFLPGRMAYVVDLDDEYADTDIPTTLIRSKADCPTMEAQTTLTTNDIVI
          ..LGRNVYRMLFKSKAYE.NELFLPGRMAYVVDLDDEYADTDIP.TLIRSKADCPTMEAQTTLTT.DIVI
Retrocopy IHLGRNVYRMLFKSKAYEWNELFLPGRMAYVVDLDDEYADTDIPITLIRSKADCPTMEAQTTLTTSDIVI

Parental  SKLTQILSYLRQGT
          SKLTQILSYLRQGT
Retrocopy SKLTQILSYLRQGT

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Sorex araneus was not studied using RNA-Seq expression data.

ChIP-Seq

Sorex araneus was not studied using ChIP-Seq data.

EST

Sorex araneus was not studied using EST data.

TSS

Sorex araneus was not studied using FANTOM5 data.

Lab

retro_sara_419 was not experimentally validated.

Homology

Retrocopy orthology:

Sorex araneus 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 8 parental genes, and 15 retrocopies.

Species	Parental gene accession	Retrocopies number
Dasypus novemcinctus	ENSDNOG00000009727	3 retrocopies	retro_dnov_618, retro_dnov_714, retro_dnov_960,
Dipodomys ordii	ENSDORG00000006584	4 retrocopies	retro_dord_128, retro_dord_130, retro_dord_134, retro_dord_139,
Homo sapiens	ENSG00000113141	1 retrocopy	retro_hsap_2262,
Gorilla gorilla	ENSGGOG00000013374	1 retrocopy	retro_ggor_1685,
Loxodonta africana	ENSLAFG00000008152	1 retrocopy	retro_lafr_362,
Otolemur garnettii	ENSOGAG00000014281	1 retrocopy	retro_ogar_1402,
Pongo abelii	ENSPPYG00000015861	1 retrocopy	retro_pabe_1954,
Sorex araneus	ENSSARG00000007388	3 retrocopies	retro_sara_416, retro_sara_419 , retro_sara_558,