RetrogeneDB ID: retro_sscr_361

Retrocopy location

• Organism: Pig (Sus scrofa)
• Coordinates: 13:203863062..203864596(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: TOX4
• Ensembl ID: ENSSSCG00000029203
• Aliases: None
• Description: TOX high mobility group box family member 4 [Source:HGNC Symbol;Acc:20161]

Sequence

>retro_sscr_361
GACTTGGATCATTCTATAGGAGCTCAGTATAGCGCTAACCCACCTGTTGCAATCGATGTACCAGTGACAGACATGACCTC
TGGCTTGGATGGGGCATAGCCAGTTGACCACCATTGACCAGTCAGAACTGAGTTCTCAACTTGGTTTGAGCTTGGGGGGG
GCCCCATCCTGCCACCTGCCCAGTCACCTGAGGATCATCTTTCAACCACCCCCTTCACTTACTAGTTCACTTCATGAGGA
TGGTGTTGAGGAATTCCAGAGGCAACTTCCCAGCCAGAAGACAGTTTTGGTGGAAGCAGGGAAAAAACAGAAGGCTCCAA
AGAGAAAAAAGAAAGATCCTAATGAACCTCAAAAACCAGTCGCAGCATATGTTTTGTTCTTTCGTGACACACAAGCTGCC
ATCAAGGGACAGAATCCCAATGCCACTTTTGGGGAGGTTTCAAAAATTGTGGCCTCCATGTGAGACAGTCTTGGAGAGGA
GCAAAAGCAGGTGTACAAGAGAAAAACTGAAGCTGCCAAGAAAGAGTATGTGAAGGCTCTGGCTGCTTATAAAGGTAATC
AGGAGTGCCAGGCCACTGTGGAAACAGTGGAATTGGATCCAGCACCACCATCACAGACTCCTTCTTCACCTCCCGTGGCC
ACTACTGCTGACCCAGCATCTCCAGCACCAGCCATGACAGAGCCCCCTGCCCTATCTCCTTCCATTGTTGTTAATTCCAC
TCTTTCATCCTATGTGACAAACCAAGCATCTTCTGGAGCTGGGGGTCAGCCCAGTATTACCAAGTTGATTATTACCAAAC
AGATGTTGCCCCCTTCTGTTACTATGTATCAAGGAGGGATGGTTACCTTTATCCCAGCAACAGTGGTGACCTCCTGGGAG
CTCCAACTAGGTCAAACCAGTACAGCTACTACCAAGCCTAGTCAACAAGCCCAGATCATCACTCGGTCCATGCTGCAGGC
AGCAGCAGCAGCAGCTTCTATGCAACTGCTTCCACCGCGACTACAACCCCCTCCATTGCCACAGATGCCTCAGCCCCCTG
CTCAGCAACAAGTGACCATTCTGCAGCAGCTTCCCCCACTCCAAGCCATGCAAAAGCCTCCACCACAGAAATTTCGAATC
AATTTACAGCAACAGCCACCTCCACGTCAGGTCAAGATTGTGCCTCCACCCACTCTGAAAATGCAGACTACCTTAGTTCC
ACCCCCCGTAGAAAACAGTCCTGAGCCTATGAACAGCAGCCCTGAGGCCCACACTGCAGAGAAAACCTCTTCTGAGACAA
TCTGTGAGATGATCACAGACGGAGTTCCTGAGGTTGCGTCTCCTCCCCAAATGGATGTTGAGTAAGTGGATGAGTCTCCC
GTGAGGCTCTCACCCCAGCCTCAATGTGTGAAGTCTGGCTGTGAGAATCCTCCCGTTGTGAGGAAAGACTGGGGCACTGA
GTAATGCAGCACTGAGTATGTGGTGAAGCACAGCAGGGATGTCTTCTCGGCCTGGGTAGCCTCTAGAAATTCAAACACAG
TGGTGGTTGTGAAA

Alignment

ORF - retro_sscr_361 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 88.59 %
• Parental protein coverage: 82.9 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  DLDHSIGTQYSANPPVTIDVPMTDMTSGL-MGHSQLTTIDQSELSSQLGLS-LGGGTILPPAQSPEDRLS
          DLDHSIG.QYSANPPV.IDVP.TDMTSGL.MGHSQLTTIDQSELSSQLGLS.L....ILPPAQSPED.LS
Retrocopy DLDHSIGAQYSANPPVAIDVPVTDMTSGL>MGHSQLTTIDQSELSSQLGLS<LXXXPILPPAQSPEDHLS

Parental  TTP-SPTSSLHEDGVEEFRRQLPSQKTVVVEAGKKQKAPKKRKKKDPNEPQKPVSAYALFFRDTQAAIKG
          TTP.S.TSSLHEDGVEEF.RQLPSQKTV.VEAGKKQKAPK.RKKKDPNEPQKPV.AY.LFFRDTQAAIKG
Retrocopy TTP>SLTSSLHEDGVEEFQRQLPSQKTVLVEAGKKQKAPK-RKKKDPNEPQKPVAAYVLFFRDTQAAIKG

Parental  QNPNATFGEVSKIVASMWDSLGEEQKQVYKRKTEAAKKEYLKALAAYKDNQECQATVETVELDPAPPSQT
          QNPNATFGEVSKIVASM.DSLGEEQKQVYKRKTEAAKKEY.KALAAYK.NQECQATVETVELDPAPPSQT
Retrocopy QNPNATFGEVSKIVASM*DSLGEEQKQVYKRKTEAAKKEYVKALAAYKGNQECQATVETVELDPAPPSQT

Parental  PSPPPVATTADPASPAPATTEPPALSPSIVVNSTLSSYVTNQASSGAGGQPNITKLIITKQMLPSSITMS
          PS.PPVATTADPASPAPA.TEPPALSPSIVVNSTLSSYVTNQASSGAGGQP.ITKLIITKQMLP.S.TM.
Retrocopy PSSPPVATTADPASPAPAMTEPPALSPSIVVNSTLSSYVTNQASSGAGGQPSITKLIITKQMLPPSVTMY

Parental  QGGMVTVIPATVVTSRGLQLGQTSTATIQPSQQAQIVTRSVLQAAAAAAASMQLPPPRLQPPPLQQMPQP
          QGGMVT.IPATVVTS..LQLGQTSTAT..PSQQAQI.TRS.LQ.AAAAAASMQL.PPRLQPPPL.QMPQP
Retrocopy QGGMVTFIPATVVTSWELQLGQTSTATTKPSQQAQIITRSMLQ-AAAAAASMQLLPPRLQPPPLPQMPQP

Parental  PTQQQVTILQQPPPLQAMQQPPPQKFRINLQQQPPPLQVKIVPPPTLKMQTTLVPPPVENSPEQPMNSSP
          P.QQQVTILQQ.PPLQAMQ.PPPQKFRINLQQQPPP.QVKIVPPPTLKMQTTLVPPPVENSPE.PMNSSP
Retrocopy PAQQQVTILQQLPPLQAMQKPPPQKFRINLQQQPPPRQVKIVPPPTLKMQTTLVPPPVENSPE-PMNSSP

Parental  EAHTVEETSPETICEMITDVVPEVESPPQMDVELVDESPVTLSPQPRCVRSGCENPPVVSKDWDNEYCSN
          EAHT.E.TS.ETICEMITD.VPEV.SPPQMDVE.VDESPV.LSPQP.CV.SGCENPPVV.KDW..E.CS.
Retrocopy EAHTAEKTSSETICEMITDGVPEVASPPQMDVE*VDESPVRLSPQPQCVKSGCENPPVVRKDWGTE*CST

Parental  ECVVKHCRDVFLAWVASRNSNTVVFVK
          E.VVKH.RDVF.AWVASRNSNTVV.VK
Retrocopy EYVVKHSRDVFSAWVASRNSNTVVVVK

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	59.99 RPM
SRP014902_testis	0.14 RPM	35.93 RPM
SRP018288_heart	0.03 RPM	28.34 RPM
SRP018288_kidney	0.00 RPM	37.04 RPM
SRP018288_liver	0.00 RPM	27.82 RPM
SRP018288_lung	0.00 RPM	89.61 RPM
SRP018856_adipose	0.15 RPM	92.06 RPM
SRP035408_brain	0.03 RPM	13.09 RPM
SRP035408_liver	0.00 RPM	12.07 RPM

ChIP-Seq

Sus scrofa was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_sscr_361 retrocopy.

TSS

Sus scrofa was not studied using FANTOM5 data.

Lab

retro_sscr_361 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_sscr_361 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

Parental genes homology involve 11 parental genes, and 13 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000006261	1 retrocopy	retro_amel_858,
Canis familiaris	ENSCAFG00000005647	2 retrocopies	retro_cfam_1625, retro_cfam_1698,
Choloepus hoffmanni	ENSCHOG00000000714	2 retrocopies	retro_chof_2239, retro_chof_631,
Homo sapiens	ENSG00000092203	1 retrocopy	retro_hsap_2970,
Macropus eugenii	ENSMEUG00000010501	1 retrocopy	retro_meug_1384,
Mustela putorius furo	ENSMPUG00000000181	1 retrocopy	retro_mputfur_718,
Mus musculus	ENSMUSG00000016831	1 retrocopy	retro_mmus_11,
Nomascus leucogenys	ENSNLEG00000014556	1 retrocopy	retro_nleu_2027,
Pongo abelii	ENSPPYG00000005598	1 retrocopy	retro_pabe_2463,
Pan troglodytes	ENSPTRG00000006126	1 retrocopy	retro_ptro_2008,
Sus scrofa	ENSSSCG00000029203	1 retrocopy	retro_sscr_361 ,