RetrogeneDB ID: retro_chof_904

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_1664:55..1183(-)
• 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_904
ATCATCAAGTCCAACTATTATGGCCTCCCAGCATGTTGTGTGAAAAGGATCATTGGTCAGGTTCTTCGAGATTTAGATTA
TCTACATTGTAAGTGTGAGACCAGTCATACTAACATAAAGCTGGAAAACATCTTGATGTGTGTGGACAATCCACACGGGA
AAAGAGTGACAGGAGAGGCCACCAAGGGGCAGAAAGCAGGTGTTCCTCCTTCTGTGTCTGCAGTGAGTATGGCTCCACAG
CAAAACCCTACAGAAAAAACATCTAGGAACAAAAAGAAAAGCTGAAAAAGAAACAGAAGTCAGCTGAGTTAGTGGAAAAA
CACCTGCATGAAATAGAGAAATTGGAGGAAGAAGCTGAAAGGAAAATAATAGGAGAAAACATCACATCAGCTGTACCTTC
CAATGAGCAAGATGAGGAATACTGCTCAGAGGTGAAACTAAAAACAGCAGAATTAGAGAAGCCTGCTGAGGGAGAGACTG
AGAATGACAACAGTAAAGCTGAGGATCAGGAAGAGAAAGAAGATTCTGAGAAAGAAAACATTGAGACAGATGAAGATGAT
GGTGAACAGGAACTTGTGAACATAGACCCTATGTGGGTAGAATCACCCAAAAATAATAGCCATAATGAGAATGGCCCATT
CATAGTGGAAAAGCAGTTAGATGATGATGAAGAAGAAGATGGCCCAAATCCTGAGGAATATAACCTTGATGAGCCAAATG
CAGAAAGTGCTGATACATATAGCAGCCCTTATGAACAATTTAATGGTGAATTGCCAAATGGACAACATAAAATTCCAGAG
TCACAGTTTCCAGAATTTTGCACTTCATCATTCTCTGGGCCCTTAGACCCTGTGGCATGTGGCTTTGTGCTTTCTGAGGG
ATCCCCACTTATTGAGCAAGAGAAAAGCCATCCATCCCATGACAGAAGCAGGACAGTTTCAGCCTCCAGTACTGAGGATT
TGCCAACAAAAGAAAAAAGTACCCTGGGCAGCTGACTTTCTGGTGACCCCCCTCAATCCATGGAATGCAGATAAAATTAG
AGTTTAAATGGCCATCCTGAGAAATGCTTGTTGGCTGCATAAACACTTCATAGAAGATATCCATATGTGTCAGTATAGAT
CCATAGAG

Alignment

ORF - retro_chof_904 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 70.42 %
• Parental protein coverage: 56.59 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  IIKSNYQGLPVRCVKSIIRQVLQGLDYLHSKCKIIHTDIKPENILMCVDDAYVRRMAAEATEWQKAGAPP
          IIKSNY.GLP..CVK.II.QVL..LDYLH.KC...HT.IK.ENILMCVD.....R...EAT..QKAG.PP
Retrocopy IIKSNYYGLPACCVKRIIGQVLRDLDYLHCKCETSHTNIKLENILMCVDNPHGKRVTGEATKGQKAGVPP

Parental  PSGSAVSTAPQQKPIGKISKNKKK-KLKKKQKRQAELLEKRLQEIEELEREAERKIIEENITSAVPSNEQ
          .S.SAVS.APQQ.P..K.S.NKKK.KLKKKQK..AEL.EK.L.EIE.LE.EAERKII.ENITSAVPSNEQ
Retrocopy -SVSAVSMAPQQNPTEKTSRNKKK<KLKKKQK-SAELVEKHLHEIEKLEEEAERKIIGENITSAVPSNEQ

Parental  DEDYCSGLKLKTAELEESAEGETENDNGQAEDQEEKEDAEKENIEKGEDDVEQELVNIDPTWIESPKTNG
          DE.YCS..KLKTAELE..AEGETENDN..AEDQEEKED.EKENIE..EDD.EQELVNIDP.W.ESPK.N.
Retrocopy DEEYCSEVKLKTAELEKPAEGETENDNSKAEDQEEKEDSEKENIETDEDDGEQELVNIDPMWVESPKNNS

Parental  HIENGPFLLEQQLDDEDEDEEDCPNPEEYNLDEPNAESDYTYSSSYEQFNGELPNGQHKIPESQFPEFST
          H.ENGPF..E.QLDD..E..ED.PNPEEYNLDEPNAES..TYSS.YEQFNGELPNGQHKIPESQFPEF.T
Retrocopy HNENGPFIVEKQLDDDEE--EDGPNPEEYNLDEPNAESADTYSSPYEQFNGELPNGQHKIPESQFPEFCT

Parental  SLFSGPLDPVACGSALSEGSPLT--EQEEGSPSHDRSRTVSASSTGDLPKTKTR-AADLLVNPLDPRNAD
          S.FSGPLDPVACG..LSEGSPL...E....S....R....S...........T..AAD.LV.PL.P.NAD
Retrocopy SSFSGPLDPVACGFVLSEGSPLIEQEKSHPSHDRSRTVSASSTEDLPTKEKSTL>AADFLVTPLNPWNAD

Parental  KIRVKIADLGNACWVHKHFTEDIQTRQYRSIE
          KIRV..A.L.NACW.HKHF.EDI...QYRSIE
Retrocopy KIRV*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_904 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,