RetrogeneDB ID: retro_chof_2

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_1791:17852..19073(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCHOG00000011281
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: SLC5A1
• Ensembl ID: ENSCHOG00000005940
• Aliases: None
• Description: solute carrier family 5 (sodium/glucose cotransporter), member 1 [Source:HGNC Symbol;Acc:11036]

Sequence

>retro_chof_2
ATGAGGGCTGTGCTGGAGACAGCAGACATTGCCATAGTGGCTCTGTATTTTATCCTGGTCATGTGCATTGGTTTTTTTGC
CATGTGGAAATCTAATAGAAGCACCGTGAGTGGATACTTCCTGGCGGGGCGCTCTATGACCTGGGTAGCTATTGGTGCCT
CTCTATTTGTGAGCAATATTGGGAGTGAGCACTTCATTGGGCTGGCAGGATCTGGAGCTGCGAGTGGATTTGCAGTGGGC
GCATGGGAATTCAATGCCTTACTGCTTTTGCAACTTCTGGGATGGGTTTTCATCCCAATATACATCCGGTCAGGGGTATA
TACCATGCCTGAATACTTGTCCAAGCGATTTGGTGGCCATAGGATTCAGGTCTATTTTGCAGCCTTGTCTCTGATTCTAT
ATATTTTCACCAAACTCTCAGTGGATCTGTATTCGGGTGCCCTGTTTATCCAGGAGTCTTTGGGTTGGAATCTTTACGTG
TCTGTCATCCTGCTCATTGGCATGACTGCCTTGCTGACTGTCACCGGAGGCCTTGTTGCAGTGATCTACACAGACACTCT
GCAGGCTCTGCTTATGATTATTGGCGCACTCACACTTATGATTATTAGCATAATGGAGATTGGTGGGTTTGAGGAAGTTA
AGAGAAGGTACATGTTGGCCTCACCCAATGTCACCTCCATCTTGTTGACATACAACCTTTCCAACACAAATTCTTGTAAT
GTCAACCCTAAGGAAGATGCCCTGAAAATGTTGCGGAATCCGACAGATGAAGATGTTCCTTGGCCTGGATTTGTTCTTGG
GCAGACCCCAGCTTCAGTATGGTACTGGTGTGCTGACCAAGTCATCGTGCAGAGGGTTCTAGCCGCCAAAAACATTTCTC
ATGCCAAAGGCTCTACTCTTATGGCTGGCTTCTTGAAGCTTCTGCCAATGTTTATCATAGTGGTCCCAGGAATGATCTCG
AGGATACTGTTTACTGATGACATAGCTTGCATCAACCCAGAACACTGCATGCAAGTGTGTGGAAGCAGAGCTGGGTGCTC
CAACATTGCCTACCCACGCCTGGTGATGAAGCTGGTTCCTGTGGGCCTCCGGGGACTAATGATGGCAGTGATGATTGCAG
CTCTAATGAGTGACTTGGACTCTATATTTAACAGTGCCAGTACCATATTCACCCTTGATGTGTACAAACTCATCCGCAAG
AGTGCAAGCTCCCGGGAACTA

Alignment

ORF - retro_chof_2 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 53.11 %
• Parental protein coverage: 58.2 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  ALILVVVLGWVFVPIYIKAGVVTMPEYLRKRFGGQRIQIYLSILSLLLYIFTKISADIFSGAIFINLALG
          AL.L...LGWVF.PIYI..GV.TMPEYL.KRFGG.RIQ.Y...LSL.LYIFTK.S.D..SGA.FI...LG
Retrocopy ALLLLQLLGWVFIPIYIRSGVYTMPEYLSKRFGGHRIQVYFAALSLILYIFTKLSVDLYSGALFIQESLG

Parental  LDLYLAIFILLLITGLYTITGGLAAVIYTDTLQTVIMLVGSFILTGFAFYEVGGYETFMTKYMNAIP---
          ..LY.....L...T.L.T.TGGL.AVIYTDTLQ...M..G...L......E.GG.E.....YM.A.P...
Retrocopy WNLYVSVILLIGMTALLTVTGGLVAVIYTDTLQALLMIIGALTLMIISIMEIGGFEEVKRRYMLASPNVT

Parental  TLISDGNITVKKEC-YTPRADSFHIFRDPLEGDLPWPGLIFGLSIIALWYWCTDQVIVQRCLSAKNMSHV
          ......N......C...P..D.....R.P...D.PWPG...G......WYWC.DQVIVQR.L.AKN.SH.
Retrocopy SILLTYNLSNTNSCNVNPKEDALKMLRNPTDEDVPWPGFVLGQTPASVWYWCADQVIVQRVLAAKNISHA

Parental  KAGCIMCGYLKLLPMFLMVMPGMISP--YTEKVACVLPSECKKFCGTEVGCTNIAYPTLVVELMPDGLRG
          K....M.G.LKLLPMF..V.PGMIS....T...AC..P..C...CG...GC.NIAYP.LV..L.P.GLRG
Retrocopy KGSTLMAGFLKLLPMFIIVVPGMISRILFTDDIACINPEHCMQVCGSRAGCSNIAYPRLVMKLVPVGLRG

Parental  LMLSVMLASLMSSLTSIFNSASTLFTMDIYTKVRKRASEKEL
          LM..VM.A.LMS.L.SIFNSAST.FT.D.Y...RK.AS..EL
Retrocopy LMMAVMIAALMSDLDSIFNSASTIFTLDVYKLIRKSASSREL

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_2 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 14 parental genes, and 14 retrocopies.

Species	Parental gene accession	Retrocopies number
Anas platyrhynchos	ENSAPLG00000007944	1 retrocopy	retro_apla_5,
Choloepus hoffmanni	ENSCHOG00000005940	1 retrocopy	retro_chof_2 ,
Callithrix jacchus	ENSCJAG00000011369	1 retrocopy	retro_cjac_2033,
Ficedula albicollis	ENSFALG00000007384	1 retrocopy	retro_falb_29,
Homo sapiens	ENSG00000100170	1 retrocopy	retro_hsap_105,
Gallus gallus	ENSGALG00000006728	1 retrocopy	retro_ggal_2,
Monodelphis domestica	ENSMODG00000009915	1 retrocopy	retro_mdom_1324,
Mustela putorius furo	ENSMPUG00000012749	1 retrocopy	retro_mputfur_837,
Oryctolagus cuniculus	ENSOCUG00000017569	1 retrocopy	retro_ocun_1633,
Otolemur garnettii	ENSOGAG00000003370	1 retrocopy	retro_ogar_2513,
Ochotona princeps	ENSOPRG00000010458	1 retrocopy	retro_opri_6,
Procavia capensis	ENSPCAG00000015157	1 retrocopy	retro_pcap_3,
Rattus norvegicus	ENSRNOG00000017775	1 retrocopy	retro_rnor_794,
Ictidomys tridecemlineatus	ENSSTOG00000006386	1 retrocopy	retro_itri_13,