RetrogeneDB ID: retro_chof_1584

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_33181:5396..6525(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SRPK2
• Ensembl ID: ENSCHOG00000000641
• Aliases: None
• Description: SRSF protein kinase 2 [Source:HGNC Symbol;Acc:11306]

Sequence

>retro_chof_1584
ATCATCAAGTCCAACTATTACGGCCTCCCAGCATGTTGTGTGAAAAGGATCATTGGTCAGGTTCTTCAAGATTTAGATTA
TCTACATTGTAAGTGTGAGACCAGTCATACTAACATAAAGCTGGAAAACATCTTGATGTGCGTGGACAATCCACACGGGA
AAAGAGTGACAGGAGAGGCCACCAAGGGGCAGAAAGCAGGTGTTTTTCCTTCTGTGTCTGCAGTGAGTATGGCTCCACAG
CAAAACCCTGCAGAAAAAATATCTATAAACAAAAAGAGAAGCTGAAAAAGAAACAGAAGTCAGCTGAGTTAGTGGAAAAA
ACACCTGCATGAAATAGAGAAATTGGAGGAAGAAGCTGAAAGGAAAATAATAGGAGAAAACATCACATCAGCTGTACCTT
CCAATGAGCAAGATGAGGAATACTGCTCAGAGGTGAAACTAAAAACAGCAGAATTAGAGAAGCCTGCTGAGGGAGAGACT
AAGAATGACAACAGTAAAGCTGAGGATCAGGAAGAGAAAGAAGATTCTGAGAAAGAAAACATTGAAACAGATGAAGATGA
TGGTGAACAGGAACTTGTGAACATAGACCCTATGTGGGTAGAATCACCCAAAAACAATAGCCATAATGAGAATGGCCCAT
TCATACTGGAAAAGCAGTTAAATGATGATGATGAAGAAGATGGCCCAAATCCTGAGGAATATAACCTTGATGAGCCAAAC
GCAGAAAGTGCTTATATATATAGCAGCTCTTATGAACAATTTAATGGTGAATTGCCAAATGGGCAACATAAAATTCCAGA
GTCACAGTTTCCAGAATTTTGCACTTCATCATTCTCTGGGCCCTTAGACCCTGTGGCATGTGGCTTTGTGCTTTCTGAGG
GATCCCCACTTATTGAGCAAGAGAAAAGCCATCCATCCCATGACAGAAGCAGGACAGTTTCAGCCTCCAGTACTGAGGAT
TTGCCAACAAAAGAAAAAAGTACCCTGGGCAGCTGACTTTCTGGTGACCCCCCTCAATCCATGGAATGCAGATAAAATTA
GAGTTTAAATGGCCATCCTGAGAAATGCTTGTTGGCTGCATAAACACTTCATAGAAGATATCCATATGTGTCAGTATAGA
TCCATAGAG

Alignment

ORF - retro_chof_1584 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 70.5 %
• Parental protein coverage: 56.59 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  IIKSNYQGLPVRCVKSIIRQVLQGLDYLHSKCKIIHTDIKPENILMCVDDAYVRRMAAEATEWQKAGAPP
          IIKSNY.GLP..CVK.II.QVLQ.LDYLH.KC...HT.IK.ENILMCVD.....R...EAT..QKAG..P
Retrocopy IIKSNYYGLPACCVKRIIGQVLQDLDYLHCKCETSHTNIKLENILMCVDNPHGKRVTGEATKGQKAGVFP

Parental  PSGSAVSTAPQQKPIGKISKNKKK-KLKKKQKRQAELLEK-RLQEIEELEREAERKIIEENITSAVPSNE
          .S.SAVS.APQQ.P..KIS.NKK..KLKKKQK..AEL.EK..L.EIE.LE.EAERKII.ENITSAVPSNE
Retrocopy -SVSAVSMAPQQNPAEKISINKKR<KLKKKQK-SAELVEK>HLHEIEKLEEEAERKIIGENITSAVPSNE

Parental  QDEDYCSGLKLKTAELEESAEGETENDNGQAEDQEEKEDAEKENIEKGEDDVEQELVNIDPTWIESPKTN
          QDE.YCS..KLKTAELE..AEGET.NDN..AEDQEEKED.EKENIE..EDD.EQELVNIDP.W.ESPK.N
Retrocopy QDEEYCSEVKLKTAELEKPAEGETKNDNSKAEDQEEKEDSEKENIETDEDDGEQELVNIDPMWVESPKNN

Parental  GHIENGPFLLEQQLDDEDEDEEDCPNPEEYNLDEPNAESDYTYSSSYEQFNGELPNGQHKIPESQFPEFS
          .H.ENGPF.LE.QL.D.DE..ED.PNPEEYNLDEPNAES.Y.YSSSYEQFNGELPNGQHKIPESQFPEF.
Retrocopy SHNENGPFILEKQLNDDDE--EDGPNPEEYNLDEPNAESAYIYSSSYEQFNGELPNGQHKIPESQFPEFC

Parental  TSLFSGPLDPVACGSALSEGSPLT--EQEEGSPSHDRSRTVSASSTGDLPKTKTR-AADLLVNPLDPRNA
          TS.FSGPLDPVACG..LSEGSPL...E....S....R....S...........T..AAD.LV.PL.P.NA
Retrocopy TSSFSGPLDPVACGFVLSEGSPLIEQEKSHPSHDRSRTVSASSTEDLPTKEKSTL>AADFLVTPLNPWNA

Parental  DKIRVKIADLGNACWVHKHFTEDIQTRQYRSIE
          DKIRV..A.L.NACW.HKHF.EDI...QYRSIE
Retrocopy DKIRV*MAILRNACWLHKHFIEDIHMCQYRSIE

Legend:

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

Expression

RNA-Seq

Choloepus hoffmanni was not studied using RNA-Seq expression data.

ChIP-Seq

Choloepus hoffmanni was not studied using ChIP-Seq data.

EST

Choloepus hoffmanni was not studied using EST data.

TSS

Choloepus hoffmanni was not studied using FANTOM5 data.

Lab

retro_chof_1584 was not experimentally validated.

Homology

Retrocopy orthology:

Choloepus hoffmanni 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 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000000641	2 retrocopies	retro_chof_1584 , retro_chof_904,
Macaca mulatta	ENSMMUG00000022732	1 retrocopy	retro_mmul_2292,