RetrogeneDB ID: retro_sscr_417

Retrocopy location

• Organism: Pig (Sus scrofa)
• Coordinates: 14:71303209..71304079(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: OTX2
• Ensembl ID: ENSSSCG00000005063
• Aliases: None
• Description: orthodenticle homeobox 2 [Source:HGNC Symbol;Acc:8522]

Sequence

>retro_sscr_417
ATGATGTCTTATCTTAGGCAACCACTTTACGCAGTCAATGGGTTAAATCTGACCACTTCAAGCATGGACTTGCTACACTC
CTCAGTGAGGTACCCAGTCACTCCTCGGAAACAGTGGCGGGAGAGGATGACATTCACCCAGGTGCAGCTAGATGCGCTGG
AAGCACTGTTTGCTAAGACCTGATACCCAGACATCTTCAGGCAGGAGGAGATGGAGCCGAAAATCAACTTGCCCAAGTCC
AGGGTGCAGGTATTGTTTAGAATGGAAGAGCTAAGTGCAGCCAACAGCAGCAGCAGCAACAGAATGAAGGTCAAAACAAA
GTGAGACCTGTCAAAAAGAAGACATTTCCTTCCTGGGAAGTGAGTTTAGAGAGTGGAACAAGTGGTCAATTCACTCCCCG
CCTCTAGCACCTCAATCCTGGCCATTTCCAGCAGCAGTGCTCCTGTGTTTATTTGGATCCAGCTTCCATCTCCCCACTAC
CAAACCCCTTGTCCGCCTACTTTTCCTGCATGCAGAGGTCCTATCCCATGAGCTATACTCAGGCTTCAGGTTATAGTCAA
GGATATGCTGGCTCAACTTCCTACTTTGGGGGCATGGACTGTGGATCTTATTTGACCCCTGTGGATCACCAGCTTCCTGG
ACAAGGGACCATACTCAGTCCCATGGGTACCAATGCAGTTAAAAACAGCCATCTCAATCAGTCCCCAGCTTCTCTGTCTA
CCTCAGGGATATGGAGCTTCAAGCTTGGGTTTTAACTCAACCACTGATTGCTTGGATTATAAGGACCAAACTGCCTCCTG
GAAGCTTAATTTCAATGCTGACTACTTGGATTAAAAAGATCAGACATCCTTGTGGAAATTCCAGGTTTTG

Alignment

ORF - retro_sscr_417 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 81.97 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 2
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  MMSYLKQPPYAVNGLSLTTSGMDLLHPSVGYPATPRKQRRERTTFTRAQLDVLEALFAKTRYPDIFMREE
          MMSYL.QP.YAVNGL.LTTS.MDLLH.SV.YP.TPRKQ.RER.TFT..QLD.LEALFAKT.YPDIF..EE
Retrocopy MMSYLRQPLYAVNGLNLTTSSMDLLHSSVRYPVTPRKQWRERMTFTQVQLDALEALFAKT*YPDIFRQEE

Parental  VALKINLPESRVQVWFK-NRRAKCRQQQQQQQNGGQNKVRPAKKKTSPAREVSSESGTSGQFTP-PSSTS
          ...KINLP.SRVQV.F..N.RAKC.QQQQQQQN.GQNKVRP.KKKT.P..EVS.ESGTSGQFTP..SSTS
Retrocopy MEPKINLPKSRVQVLFR<NGRAKCSQQQQQQQNEGQNKVRPVKKKTFPSWEVSLESGTSGQFTP>ASSTS

Parental  VPAISSSSAPVSIW-SPASISPLSDPLSTSSSCMQRSYPMTYTQASGYSQGYAGSTSYFGGMDCGSYLTP
          ..AISSSSAPV.IW..PASISPL..PLS...SCMQRSYPM.YTQASGYSQGYAGSTSYFGGMDCGSYLTP
Retrocopy ILAISSSSAPVFIW<DPASISPLPNPLSAYFSCMQRSYPMSYTQASGYSQGYAGSTSYFGGMDCGSYLTP

Parental  MHHQLPGPGTTLSPMGTNAV-TSHLNQSPASLST-QGYGASSLGFNSTTDCLDYKDQTASWKLNFNADCL
          ..HQLPG.GT.LSPMGTNAV..SHLNQSPASLST.QGYGASSLGFNSTTDCLDYKDQTASWKLNFNAD.L
Retrocopy VDHQLPGQGTILSPMGTNAVKNSHLNQSPASLST>QGYGASSLGFNSTTDCLDYKDQTASWKLNFNADYL

Parental  DYKDQTSSWKFQVL
          D.KDQTS.WKFQVL
Retrocopy D*KDQTSLWKFQVL

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
SRP014902_placenta	0.00 RPM	0.00 RPM
SRP014902_testis	0.00 RPM	1.13 RPM
SRP018288_heart	0.00 RPM	0.00 RPM
SRP018288_kidney	0.00 RPM	0.00 RPM
SRP018288_liver	0.00 RPM	0.00 RPM
SRP018288_lung	0.00 RPM	0.00 RPM
SRP018856_adipose	0.00 RPM	0.17 RPM
SRP035408_brain	0.00 RPM	0.00 RPM
SRP035408_liver	0.00 RPM	0.00 RPM

ChIP-Seq

Sus scrofa was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_sscr_417 retrocopy.

TSS

Sus scrofa was not studied using FANTOM5 data.

Lab

retro_sscr_417 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_sscr_417 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 5 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000014741	1 retrocopy	retro_btau_687,
Callithrix jacchus	ENSCJAG00000018583	1 retrocopy	retro_cjac_1380,
Cavia porcellus	ENSCPOG00000003420	1 retrocopy	retro_cpor_149,
Sus scrofa	ENSSSCG00000005063	1 retrocopy	retro_sscr_417 ,
Tursiops truncatus	ENSTTRG00000004650	1 retrocopy	retro_ttru_473,