RetrogeneDB ID: retro_sara_416

Retrocopy location

• Organism: Shrew (Sorex araneus)
• Coordinates: scaffold_196585:5632..6517(+)
• 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_416
AGAGAGCCGTTTTCCAATCCGTTGGCCCCAGATGGCTACGATGTGGACGATCCTCACTCCTCCCACCAATCTAAGCGCAC
CAATGAGGATTTCAGAAAACTTCTCATGACCCCAAGGGCTGCGCCTACCTCTGCACCACCCTCTAAATCACATCACCATG
AGATGCCAAGGGAGTATAATGAGAAGGAGGATCCAGCTGCGTGGAGGAGAAGAAAGAAAAATTATGAAAAACTTCGCCAA
CAAGAAATTGAGAGAGAGCGAGAGCTAGCAGAGAAATACCGGGACCGGGCCAAGGAACGAAGAGATGGTGTGAACAAAGA
TTATGAGGAAACTGAGCTGATCAGCACCACGGCAAACTACAGGGCCGTGGGCCCCACTGCTGAGGCAGACACATCAGCTG
CAGAGAAAAGACAGTTGATCCAGGAGTCCAAGTTCTTGGGTGGTGACATGGAATATACCCATTTGGTGAAAGGCTTGGAT
TTTTCTCTGCTTCAGAAGATTCGAGCTGAGATTGCCAGCAAGGAGAAAGAGGGAGAACTGATGGAAAAGCCCCAGAAGGA
AACCAAGAAAGACGAGGACCCTGAAAACAAAATTGAATTTAAAACACGTTTAGGCCGCAATGTTTACCGTATGCTCTTCA
AGAGCAAAGCGTACGAACGGAATGAGCTGTTCCTGCCAGGCCGCATGGCCTATGTGGTGGACCTGGACGATGGGTATGCG
GACACGGACATCCCCACCACTCTTATCCGAAGCAAGGCGGACTGCCCCACCGTGGAGGCCCAGACCACACTGACAACAAG
TGACATTGTCATCAGCAAGCTCACACAGATTCTTTCCTACTTGAGGCAGGGAACCCGTAACAAGAAGCTCAAGAAGAAAG
ATAAA

Alignment

ORF - retro_sara_416 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 93.29 %
• Parental protein coverage: 98.35 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  REPFSNPLAPDGHDVDDPHSFHQSKLTNEDFRKLLMTPRAAPTSAPPSKSRHHEMPREYNEDEDPAARRR
          REPFSNPLAPDG.DVDDPHS.HQSK.TNEDFRKLLMTPRAAPTSAPPSKS.HHEMPREYNE.EDPAA.RR
Retrocopy REPFSNPLAPDGYDVDDPHSSHQSKRTNEDFRKLLMTPRAAPTSAPPSKSHHHEMPREYNEKEDPAAWRR

Parental  KKKSYYAKLRQQEIERERELAEKYRDRAKERRDGVNKDYEETELISTTANYRAVGPTAEADKSAAEKRRQ
          .KK.Y..KLRQQEIERERELAEKYRDRAKERRDGVNKDYEETELISTTANYRAVGPTAEAD.SAAEKR.Q
Retrocopy RKKNY-EKLRQQEIERERELAEKYRDRAKERRDGVNKDYEETELISTTANYRAVGPTAEADTSAAEKR-Q

Parental  LIQESKFLGGDMEHTHLVKGLDFALLQKVRAEIASKEKEEEELMEKPQKETKKDEDPENKIEFKTRLGRN
          LIQESKFLGGDME.THLVKGLDF.LLQK.RAEIASKEKE..ELMEKPQKETKKDEDPENKIEFKTRLGRN
Retrocopy LIQESKFLGGDMEYTHLVKGLDFSLLQKIRAEIASKEKEG-ELMEKPQKETKKDEDPENKIEFKTRLGRN

Parental  VYRMLFKSKAYERNELFLPGRMAYVVDLDDEYADTDIPTTLIRSKADCPTMEAQTTLTTNDIVISKLTQI
          VYRMLFKSKAYERNELFLPGRMAYVVDLDD.YADTDIPTTLIRSKADCPT.EAQTTLTT.DIVISKLTQI
Retrocopy VYRMLFKSKAYERNELFLPGRMAYVVDLDDGYADTDIPTTLIRSKADCPTVEAQTTLTTSDIVISKLTQI

Parental  LSYLRQGTRNKKLKKKDK
          LSYLRQGTRNKKLKKKDK
Retrocopy LSYLRQGTRNKKLKKKDK

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_416 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,