RetrogeneDB ID: retro_btau_1458

Retrocopy location

• Organism: Cow (Bos taurus)
• Coordinates: 6:63024080..63024495(+)
• Located in intron of: ENSBTAG00000011156

Retrocopy information

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

Parental gene information

• Parental gene symbol: SFT2D1
• Ensembl ID: ENSBTAG00000002993
• Aliases: None
• Description: vesicle transport protein SFT2A [Source:RefSeq peptide;Acc:NP_001029723]

Sequence

>retro_btau_1458
CAGGTCCTGGATGCCTCTTTCCTCCATTTCCACACCAGGATTAGGTGGTTTGTCATATGCTTTCTGTGGGGCATTTTCTG
TTGGATCATTGGAACTGGATGGGTGTGGATTCCTGGAGGCATAAAACCTTCTGCAGTGTTTTACACCCTTGGAAATATTG
CTAGATCCACCAGTATATGCTTGTTAATGGGACCCGTGAAAAAACAAAGATAATGTCTGAGACAAAAAGCTGCCTGTAAC
AATGGTCATGCTTCTGTGATTAAGATTCACATCCTGTGATGCTCTTTGGTGGCATAGAAGGAGACTGGCCTTATTTCTCT
GCATATTGCAGCTCTCATCAAAGATCTTGCATAGCCTATTACGCATCTCATATGCAAGTGGTGCAGTAATTAAATGCTCT
TCTTTTCTCCTAAGT

Alignment

ORF - retro_btau_1458 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 58.16 %
• Parental protein coverage: 87.42 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  QVLDASTLSFNTRLKWFAICFVSGIFFSILGTGLLWLPGGIKLFAVFYTFGNIAALASTCFLMGPVK-QL
          QVLDAS.L.F.TR..WF.ICF..GIF..I.GTG..W.PGGIK..AVFYT.GNIA...S.C.LMGPVK...
Retrocopy QVLDASFLHFHTRIRWFVICFLWGIFCWIIGTGWVWIPGGIKPSAVFYTLGNIARSTSICLLMGPVK<KT

Parental  KKMFET-TRLLATVIMLLCFVLTLCAALWWHKKGLAVLFCILQFLSMTWYSLSYIPYARDAVIKCCSSLL
          K.M.ET...L..T..MLL....T.C.ALWWH...LA...CILQ..S....SL..I.YA..AVIKC.S.LL
Retrocopy KIMSET<KKLPVTMVMLL*LRFTSCDALWWHRRRLALFLCILQLSSKILHSLLRISYASGAVIKCSSFLL

Parental  S
          S
Retrocopy S

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
ERP005899_liver	0.00 RPM	41.02 RPM
ERP005899_muscle	0.05 RPM	64.35 RPM
SRP017611_brain	0.00 RPM	25.49 RPM
SRP017611_kidney	0.00 RPM	52.40 RPM
SRP017611_liver	0.00 RPM	11.78 RPM
SRP030211_testis	0.01 RPM	19.12 RPM

ChIP-Seq

Bos taurus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_btau_1458 retrocopy.

TSS

Bos taurus was not studied using FANTOM5 data.

Lab

retro_btau_1458 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_btau_1458 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

Parental genes homology involve 13 parental genes, and 25 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000009311	3 retrocopies	retro_amel_1244, retro_amel_1452, retro_amel_374,
Bos taurus	ENSBTAG00000002993	5 retrocopies	retro_btau_1458 , retro_btau_1460, retro_btau_31, retro_btau_546, retro_btau_900,
Canis familiaris	ENSCAFG00000000811	2 retrocopies	retro_cfam_283, retro_cfam_551,
Equus caballus	ENSECAG00000019479	1 retrocopy	retro_ecab_1029,
Mus musculus	ENSMUSG00000073468	1 retrocopy	retro_mmus_164,
Oryctolagus cuniculus	ENSOCUG00000001200	1 retrocopy	retro_ocun_1492,
Otolemur garnettii	ENSOGAG00000006302	1 retrocopy	retro_ogar_1601,
Ochotona princeps	ENSOPRG00000003408	2 retrocopies	retro_opri_37, retro_opri_809,
Pongo abelii	ENSPPYG00000017165	1 retrocopy	retro_pabe_181,
Pteropus vampyrus	ENSPVAG00000012673	3 retrocopies	retro_pvam_1340, retro_pvam_465, retro_pvam_559,
Sus scrofa	ENSSSCG00000004020	1 retrocopy	retro_sscr_751,
Tupaia belangeri	ENSTBEG00000000045	2 retrocopies	retro_tbel_3277, retro_tbel_747,
Tursiops truncatus	ENSTTRG00000004447	2 retrocopies	retro_ttru_1353, retro_ttru_624,