RetrogeneDB ID: retro_pcap_3

Retrocopy location

• Organism: Hyrax (Procavia capensis)
• Coordinates: scaffold_15186:17056..19213(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSPCAG00000006551
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: SLC5A1
• Ensembl ID: ENSPCAG00000015157
• Aliases: None
• Description: solute carrier family 5 (sodium/glucose cotransporter), member 1 [Source:HGNC Symbol;Acc:11036]

Sequence

>retro_pcap_3
ATGAGGGCTGTCCTGGAGACGGCAGACATCGCCATAGTGGCCCTGTATTTTATCCTGGTCATGTGCATTGGTTTCTTTGC
CATGTGGAAGTCTAATAGAAGCACCGTGAGTGGATACTTCCTGGCGGGGCGCTCTATGACTTGGGTGGCGATTGGTGCCT
CTCTGTTTGTGAGCAATATTGGGAGTGAACACTTCATTGGGCTGGCGGGATCTGGAGCGGCCAGCGGATTTGCGGTGGGC
GCCTGGGAGTTCAATGCCTTACTGCTTTTGCAACTTCTAGGATGGGTTTTCATCCCGATTTACATCCGGTCGGGGGTGTA
CACCATGCCCGAGTACTTGTCCAAGCGATTCGGTGGCCATAGGATTCAGGTGTATTTCGCAGCCTTGTCTCTGATCCTCT
ATATCTTCACCAAGCTTTCAGTGGATCTGTACTCGGGGGCCCTCTTTATCCAGGAGTCTTTAGGTTGGAACCTCTATGTG
TCTGTCATCCTGCTCATTGGTATGACTGCCTTGCTGACCGTCACGGGAGGCCTTGTGGCGGTCATCTACACGGACACGCT
CCAGGCTCTGCTCATGATCGTCGGGGCGCTGACCCTCATGGTGATCAGCATGATGGAGATTGGTGGGTTTGAGGAAGTTA
AGAGACGGTACATGCTGGCCTCTCCCAACGTCACTTCCATCTTGTTGACCTACAACTTGTCCAACACAAATTCTTGTAAT
GTCCACCCCAAGAAAGATGCCCTGAAGATGTTGCGGAATCCGACCGATGAGGATGTGCCTTGGCCGGGCTTCCTTCTCGG
GCAGACGCCGGCGTCGGTGTGGTACTGGTGTGCCGACCAGGTCATCGTGCAGAGGGTACTGGCGGCCAAGAACATCGCCC
ACGCCAAGGGCTCCACTCTGATGGCCGGCTTCCTGAAGCTCCTGCCGATGTTCATCATTGTGGTCCCGGGGATGATCTCC
AGGATCCTGTTTGCCGACGACCTCGCCTGCATCAACCCCGAGCACTGCGTGCAGGTGTGCGGCAGCAGGGCCGGCTGCTC
CAACATCGCCTACCCCCGCCTGGTGATGAAGCTGGTCCCCGTGGGCCTCCGGGGCCTGATGATGGCGGTGATGATCGCGG
CCCTGATGAGCGACCTTGACTCCATCTTCAACAGCGCCAGCACCATCTTCACGCTCGATGTGTACAAGCTCGTGCGCAGG
AGTGCCAGCTCCCGGGAGCTCATGGTCGTCGGGCGGATCTTCGTGGCGTTCATGGTGCTCATCAGCATCGCCTGGGTGCC
CATCATCGTGGAGATGCAGGGGGGCCAGATGTACCTGTACATTCAGGAGGTGGCCGACTACCTGACGCCCCCGGTCGCTG
CCCTTTTCCTCCTGGCCATCTTCTGGAAGCGCTGCAACGAGCAGGGGGCTTTCTATGGCGGGATGGCCGGCTTCATCCTC
GGAGCAGTGCGGCTGACGCTGGCCTTCGCCTACCGTGCCCCTGAGTGTGACCAGCCCGATAGCAGACCGGGCTTCATCAA
AGACATCCACTACATGTATGTGGCCACGGCATTATTCTGGGTCACGGGACTCATCACTGTCATCGTCAGCCTTCTCACGC
CACCTCCCACGAAGGAGCAGATCCGCACTACCACCTTCTGGTCCAAGAAGAGTGTGGTGACGAAGGAGCGCTGCTCCCCG
AAGGACGAGCCATACAAGCTGCAGGAGAAAAGCATGCTGCGGGGCGGTGAGCGCGGGGAGGCCGGCAGCCACGTCATCCC
CAACGGCAAGTCCGAAGACAGCATCAAGGCCCTTCAGCCCGAGGACGTGAATCTCCTGGTGACCCACAGGGAGGAGGCCA
ACCCGGCGGCTTCTCTGGGTCACTCGGAGGCAGAGACACCTGTGGACGCGTATTCCAATGGGCAGGCCGCTCTCATGGGG
GAGAAGGAGAGAAAGAAGGAGGTGGAGGCCGGCAGCCGATACTGGAAGTTCATAGACTGGTTCTGTGGCTTCAAGAGTAA
GAGCCTGAGCAAGAGGAGCCTCAGAGACCTGATGGAGGAGGAGGCTGTGTGCTTACAGATGCTGGAGGAGACGCCCCGCG
TGAGACTCGTCCTCAACATCGGACTCTTTGCCGTGTGTTCTCTTGGGATTTTCATGTTCGTTTATTTCTCCTTATGA

Alignment

ORF - retro_pcap_3 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 51.67 %
• Parental protein coverage: 67.02 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  LVMVVVLGWIFVPTYIRAGVVTMPEYLRKRFGGQRIQVYLSILSLILYIFTKISADIFSGAIFINLALGL
          L.....LGW.F.P.YIR.GV.TMPEYL.KRFGG.RIQVY...LSLILYIFTK.S.D..SGA.FI...LG.
Retrocopy LLLLQLLGWVFIPIYIRSGVYTMPEYLSKRFGGHRIQVYFAALSLILYIFTKLSVDLYSGALFIQESLGW

Parental  DLYVAIIVLLAVTALXXXXXGLAAVIYTDALQTAIMLVGSLILTGFAFHEVGGYEGFMEKYMKA---IPT
          .LYV..I.L...TAL.....GL.AVIYTD.LQ...M.VG.L.L......E.GG.E.....YM.A......
Retrocopy NLYVSVILLIGMTALLTVTGGLVAVIYTDTLQALLMIVGALTLMVISMMEIGGFEEVKRRYMLASPNVTS

Parental  LISDGNTTINEECYT-PRADSFHVFRDPITGDIPWPGFIFGMSILGLWYWCTDQVIVQRCLSAKNMSHVK
          .....N......C...P..D.....R.P...D.PWPGF..G......WYWC.DQVIVQR.L.AKN..H.K
Retrocopy ILLTYNLSNTNSCNVHPKKDALKMLRNPTDEDVPWPGFLLGQTPASVWYWCADQVIVQRVLAAKNIAHAK

Parental  AGCIMCGYLKLLPMFLIVMPGMISRILYTEKIACVLPSECERYCGTKVGCTNIAYPTLVVELMPNGLRGL
          ....M.G.LKLLPMF.IV.PGMISRIL.....AC..P..C...CG...GC.NIAYP.LV..L.P.GLRGL
Retrocopy GSTLMAGFLKLLPMFIIVVPGMISRILFADDLACINPEHCVQVCGSRAGCSNIAYPRLVMKLVPVGLRGL

Parental  MLSVMMASLMSSLTSIFNSASTLFTMDIYTKIRRRATEKELMIAGRLFMLVLIGISIAWVPIVQSAQSGQ
          M..VM.A.LMS.L.SIFNSAST.FT.D.Y...RR.A...ELM..GR.F......ISIAWVPI....Q.GQ
Retrocopy MMAVMIAALMSDLDSIFNSASTIFTLDVYKLVRRSASSRELMVVGRIFVAFMVLISIAWVPIIVEMQGGQ

Parental  LFDYIQSITSYLGPPIAAVFVLAIFWKRVNEPGAFWGLIIGFLVGIARMITEFAYGTGSCMEPSNCPTII
          ...YIQ....YL.PP.AA.F.LAIFWKR.NE.GAF.G...GF..G..R....FAY....C..P...P..I
Retrocopy MYLYIQEVADYLTPPVAALFLLAIFWKRCNEQGAFYGGMAGFILGAVRLTLAFAYRAPECDQPDSRPGFI

Parental  CGVHYLYFAMILFVICLIVITAVSLFTKP
          ...HY.Y.A..LF.........VSL.T.P
Retrocopy KDIHYMYVATALFWVTGLITVIVSLLTPP

Legend:

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

Expression

RNA-Seq

Procavia capensis was not studied using RNA-Seq expression data.

ChIP-Seq

Procavia capensis was not studied using ChIP-Seq data.

EST

Procavia capensis was not studied using EST data.

TSS

Procavia capensis was not studied using FANTOM5 data.

Lab

retro_pcap_3 was not experimentally validated.

Homology

Retrocopy orthology:

Procavia capensis 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,