RetrogeneDB ID: retro_cjac_2033

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 21:38118791..38120278(+)
• Located in intron of: ENSCJAG00000002867

Retrocopy information

• Ensembl ID: ENSCJAG00000002870
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: SLC5A1
• Ensembl ID: ENSCJAG00000011369
• Aliases: None
• Description: None

Sequence

>retro_cjac_2033
TTCCTGGCGGGGCGCTCTATGACTGGGATGGTCGGTGCCTCTCTGTTTGTGAGTAATATTGGGAGTGAGCACTTTAATTG
GGCTGGCAGGATCTGGAGCTGCAAGTGGATTTGCAGTGGGCGCATGGGAATTCAATGCCTTACTGCTTTTACAACTTCTG
GGATGGGTTTTTATCCCAATTTACATCCGGTCAGGTGTATATACCATGCCTGAATATTTGTCCAAGCGATTTGGTGGTCA
TAGGATTCAGGTCTATTTTGCAGCCTTGTCTCTGATTCTCTATATTTTCACCAAGCTCTCAGTGGATCTGTATTCAGGTG
CCCTCTTTATCCAGGAGTCTTTGGGTTGGAATCTTTATGTGTCTGTCATCCTGCTCATTGGCATGACTGCTTTGCTGACT
GTCACCGGAGGCCTTGTTGCAGTGATCTACACAGATACTCTACAGGCTCTGCTCATGATCGTTGGGGCACTTACACTTAT
GATTATTAGCATAATGGAGATTGGCGGGTTTGAGGAAGTTAAGAGAAGGTACATGTTGGCCTCACCCAATGTTACTTCCA
TCTTGTTGACATACAACCTTTCCAACACAAATTCTTGTAATGTCCACCCTAAGAAAGAAGCCCTGAAAATGCTGCGAGAT
CCAACAGATGAAGATGTTCCTTGGCCTGGATTCATCCTTGGGCAGACCCCAGCCTCGGTATGGTACTGGTGTGCTGACCA
AGTCATCGTGCAGAGGGTCCTTGCAGCCAAAAACATTGCTCATGCCAAAGGCTCTACTCTTATGGCTGGCTTCTTAAAGC
TTCTGCCAATGTTTATCATAGTTGTTCCAGGAATGATTTCCAGGATACTGTTTGCTGATGATATATTCTTGCATCAATCC
AGAGCACTGCATGCTAGTGTGTGGAAGCAGAGCTGGTTGCTCCAATATTGCTTACCCACGGCTGGTGATGAAGCTGGTTC
CTGTGGGCCTTCGGGGCTTAATGATGGCAGTGATGATTGCAGCTCTGATGAGTGACTTGGACTCTATCTTTAACAGTGCC
AGTACCATATTCACCCTCGATGTGTACAAACTTATCCGCAAGAGCGCAAGCTCCCGGGAGTTAATGATTGTGGGGAGGGT
TTTTGTGGCCTTTATGGTGGTGATCAGCATAGCATGGGTGCCAATCATCGTGGAGATGCAAGGAGGCCAGATGTACCTTT
ATATTCAGGAGGTAGCAGATTACCTGACACCCCCAGTGGCAGCCCTGTTCCTTCTGGCAATTTTCTGGAAGCGCTGCAAT
GAACAAGGGGCTTTCTATGGTGGAATGGCTGGGTTTGTTCTTGGAGCAATCCGTTTGATACTGGCCTTTGCCTACCGTGC
CCCAGAGTGTGACCAACCTGATAACAGGCCAGGTTTCATCAAAGACATCCATTATATGTATGTGGCCACAGTATTGTTTT
GGGTCACGGGACTCATTACTGTAATTGTGAGCCTTCTCACGCCACCT

Alignment

ORF - retro_cjac_2033 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 55.02 %
• Parental protein coverage: 73.98 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  FLAGRSMVWWPIGASLFASNIGSGHF-VGLAGTGAASGIAIGGFEWNALVLVVVLGWLFVPIYIKAGVVT
          FLAGRSM.....GASLF.SNIGS.HF..GLAG.GAASG.A.G..E.NAL.L...LGW.F.PIYI..GV.T
Retrocopy FLAGRSMTGM-VGASLFVSNIGSEHF>IGLAGSGAASGFAVGAWEFNALLLLQLLGWVFIPIYIRSGVYT

Parental  MPEYLRKRFGGQRIQVYLSVLSLLLYIFTKISADIFSGAIFINLALGLNLYLAIFLLLAITALYTITGGL
          MPEYL.KRFGG.RIQVY...LSL.LYIFTK.S.D..SGA.FI...LG.NLY....LL...TAL.T.TGGL
Retrocopy MPEYLSKRFGGHRIQVYFAALSLILYIFTKLSVDLYSGALFIQESLGWNLYVSVILLIGMTALLTVTGGL

Parental  AAVIYTDTLQTVIMLVGSLILTGFAFHEVGGYDAFMEKYMNATP---TVISDGNTTIKEECYL-PRADSF
          .AVIYTDTLQ...M.VG.L.L......E.GG.......YM.A.P.........N......C...P.....
Retrocopy VAVIYTDTLQALLMIVGALTLMIISIMEIGGFEEVKRRYMLASPNVTSILLTYNLSNTNSCNVHPKKEAL

Parental  HIFRDPLKGDLPWPGLIFGMSILALWYWCTDQVIVQRCLSAKNMSHVKAGCTLCGYLKLLPMFIMVMPGM
          ...RDP...D.PWPG.I.G......WYWC.DQVIVQR.L.AKN..H.K......G.LKLLPMFI.V.PGM
Retrocopy KMLRDPTDEDVPWPGFILGQTPASVWYWCADQVIVQRVLAAKNIAHAKGSTLMAGFLKLLPMFIIVVPGM

Parental  ISRILYTDKI-ACVVPSECEKYCGTKVGCTNIAYPTLVVELMPNGLRGLMLSVMLASLMSSLTSIFNSAS
          ISRIL..D.I..C..P..C...CG...GC.NIAYP.LV..L.P.GLRGLM..VM.A.LMS.L.SIFNSAS
Retrocopy ISRILFADDI>SCINPEHCMLVCGSRAGCSNIAYPRLVMKLVPVGLRGLMMAVMIAALMSDLDSIFNSAS

Parental  TLFTMDIYTKVRKGASEKELMIAGRLFILLLIGISIAWVPIVQSAQSGQLFDYIQSITSYLGPPIAAVFL
          T.FT.D.Y...RK.AS..ELMI.GR.F......ISIAWVPI....Q.GQ...YIQ....YL.PP.AA.FL
Retrocopy TIFTLDVYKLIRKSASSRELMIVGRVFVAFMVVISIAWVPIIVEMQGGQMYLYIQEVADYLTPPVAALFL

Parental  LGIFWKRVNEPGAFWGLILGFLIGVSRMITEFAYGTGSCMEPSNCPTIICGVHYLYFAIILFVISVISIV
          L.IFWKR.NE.GAF.G...GF..G..R.I..FAY....C..P.N.P..I...HY.Y.A..LF.......V
Retrocopy LAIFWKRCNEQGAFYGGMAGFVLGAIRLILAFAYRAPECDQPDNRPGFIKDIHYMYVATVLFWVTGLITV

Parental  VISLLTKP
          ..SLLT.P
Retrocopy IVSLLTPP

Legend:

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

Expression

RNA-Seq

Expression validation based on RNA-Seq data:

Library	Retrocopy expression	Parental gene expression
SRP051959_colon	69.16 RPM	23.87 RPM
SRP051959_heart	5.02 RPM	0.04 RPM
SRP051959_kidney	26.98 RPM	5.08 RPM
SRP051959_liver	2.84 RPM	0.24 RPM
SRP051959_lung	5.25 RPM	0.07 RPM
SRP051959_lymph_node	5.27 RPM	0.00 RPM
SRP051959_skeletal_muscle	1.86 RPM	0.00 RPM
SRP051959_spleen	3.42 RPM	0.00 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_2033 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_2033 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_2033 has 0 orthologous retrocopies within eutheria group .

---

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,