RetrogeneDB ID: retro_sscr_1006

Retrocopy location

• Organism: Pig (Sus scrofa)
• Coordinates: 8:100272053..100272682(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CLAUDIN1
• Ensembl ID: ENSSSCG00000028484
• Aliases: None
• Description: Sus scrofa claudin 1 (CLDN1), mRNA. [Source:RefSeq mRNA;Acc:NM_001244539]

Sequence

>retro_sscr_1006
GCCAACGCGGGGCTGCAGCTGCTGGGCTTCATCCTGGCCTTCCTGGGCTGGATCGGCTCCATCGTCAGCACCGCACTGCT
TCAGTGTAAGATTTACTCCTACGCTGGTGACAACATAGTGACAGTCCAGGCCATCTAGGAGGGGCTGTGGATGTCCCGCA
TGTCGCAGAGCACCGGGAAGATCCAGTGCAAAGTCTTAGACTCCTTGCTGAATCTGAACAGCACTATGCAAGCAACCCGT
GCCTTGATAGTGACTGGCATCCTTCTGGGACTATACCCATCTTTGTGGCCACCATTGGCATGAAGTGTATGAAGTGCATG
GAAGATGATGAGGTGCAGAAGATGTGGATGGCTGTCATTGGGGGAGTGATCTTTCTTATTTCAGGTCTGGCTATCTTAGT
TGCCACAGCATAGTATGGTAACAGAATTGTTCAAGAATTCTATCACCTCATGACCCCGGTCAATGCCAGATATGAATTTG
GTCAGGCTCTCTTCACTGGCTGGGCTGCTGCTTCTCTCTGCCTTCTGGGAGGTGCCCTACTTTGCCGCTCCTGTCCCCGA
AAAACAACATCTTACCCAACACAAAGGCCCTATCCAAAACCTTCACCTTCCAGTGGGAAAGACTACGTG

Alignment

ORF - retro_sscr_1006 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 82.94 %
• Parental protein coverage: 99.53 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  ANAGLQLLGFILAFLGWIGSIVSTALPQWKIYSYAGDNIVTAQAIYEGLWMSCVSQSTGQIQCKVFDSLL
          ANAGLQLLGFILAFLGWIGSIVSTAL.Q.KIYSYAGDNIVT.QAI.EGLWMS..SQSTG.IQCKV.DSLL
Retrocopy ANAGLQLLGFILAFLGWIGSIVSTALLQCKIYSYAGDNIVTVQAI*EGLWMSRMSQSTGKIQCKVLDSLL

Parental  NLNSTLQATRALMVIGILLGL-IAIFVATVGMKCMKCMEDDEVQKMRMAVIGGVIFLISGLAILVATAWY
          NLNST.QATRAL.V.GILLGL.I.IFVAT..................MAVIGGVIFLISGLAILVATA.Y
Retrocopy NLNSTMQATRALIVTGILLGL<IPIFVATIXXXXXXXXXXXXXXXXWMAVIGGVIFLISGLAILVATA*Y

Parental  GNRIVQEFYDPMTPVNARYEFGQALFTGWAAASLCLLGGALLCCSCPRKTTSYPTPRPYPKPSPSSGKDY
          GNRIVQEFY..MTPVNARYEFGQALFTGWAAASLCLLGGALLC.SCPRKTTSYPT.RPYPKPSPSSGKDY
Retrocopy GNRIVQEFYHLMTPVNARYEFGQALFTGWAAASLCLLGGALLCRSCPRKTTSYPTQRPYPKPSPSSGKDY

Parental  V
          V
Retrocopy V

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	122.78 RPM
SRP014902_testis	0.00 RPM	0.14 RPM
SRP018288_heart	0.00 RPM	0.34 RPM
SRP018288_kidney	0.00 RPM	8.18 RPM
SRP018288_liver	0.32 RPM	57.09 RPM
SRP018288_lung	0.00 RPM	3.46 RPM
SRP018856_adipose	0.02 RPM	1.41 RPM
SRP035408_brain	0.00 RPM	0.19 RPM
SRP035408_liver	0.00 RPM	14.50 RPM

ChIP-Seq

Sus scrofa was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_sscr_1006 retrocopy.

TSS

Sus scrofa was not studied using FANTOM5 data.

Lab

retro_sscr_1006 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_sscr_1006 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 2 parental genes, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Equus caballus	ENSECAG00000021074	1 retrocopy	retro_ecab_623,
Sus scrofa	ENSSSCG00000028484	1 retrocopy	retro_sscr_1006 ,