RetrogeneDB ID: retro_etel_1555

Retrocopy location

• Organism: Lesser hedgehog tenrec (Echinops telfairi)
• Coordinates: scaffold_278569:51305..52049(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RSRC1
• Ensembl ID: ENSETEG00000017217
• Aliases: None
• Description: arginine/serine-rich coiled-coil 1 [Source:HGNC Symbol;Acc:24152]

Sequence

>retro_etel_1555
ATGGGACGCCAGTCATCAGATACTGAAGAAGAAAGCCGAAGTAAGAGAAAAAAGATGCACCATAGACGGGCATCTTCAAG
TAGTTCTTCAGACAGTAGAACATATAGCCGAAAGAAAGGTGGGAGGACATCACGGTCAAAGTCAAGATCTTGGTCCAGAG
ATCTTCAGTGTCATTCACATTCTTATGGCAGAAGATGCAGGCATCGATCAAGCAGTAGCTCATCTTATGGCTCAAGAAGA
AGTCGAAGTCGATCAAGGGGTTGAGGGGAATCCTACAGAGTTCAGAGGTCTAGGTCAAAAAGCAGAACAAGAAGGTCCAG
GTCAAGACCTCGTCCACGCTCCCATAGCCGAAGCAGTGAAAGGTCCAGTCGCAGAAGAACCCGCAGTGAATCCAGAGATA
AGGAGAAGGGAGAAAAGGAGAAGGATAAGGGAAAGGACAAGGAATTGCTTGACATCAAACGTGGGGAATCGGGAAACATC
AAAGCTGGATTAGAACATCTGCCGCCAGCAGAACAGGCCACAGCCAGATTACAACTGGTTCTCTAAGCTGCTGCAAATGC
TGATGAAGCATTGAAAGCCGAAGAAAGAAATGAGGAAGAAGCAAAAAGACGAAAGGAGGAAGATCAAGCCACCCTGTTAG
AACAAGTGAAAAGAGTCAAAGAACTGGAAGCTATTGAAAGTGATTCTTTTGTTCAGCAAACATTCAGATCAAGTAAAGAA
GTCAAAAAGGCAGTGGAGCCAAGT

Alignment

ORF - retro_etel_1555 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 61.24 %
• Parental protein coverage: 79.44 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MGRRSSDTEEESRSKRKKKHRRRSSSSSSSDSRTYSRKKGGRKSRSKSRSWSRDLQFRSHSYDRRRRHRS
          MGR.SSDTEEESRSKRKK.H.RR.SSSSSSDSRTYSRKKGGR.SRSKSRSWSRDLQ..SHSY.RR.RHRS
Retrocopy MGRQSSDTEEESRSKRKKMHHRRASSSSSSDSRTYSRKKGGRTSRSKSRSWSRDLQCHSHSYGRRCRHRS

Parental  SSSSSYGSRRKRSRSRSRGRGKSYRVQRSRSKSRTRRSRSRPRPRSHSRSSERSSHRRTRSRSRDRERRK
          SSSSSYGSRR..SRSRSRG.G.SYRVQRSRSKSRTR..RSR.RPR...RS..RSS.R.....SR.R.R..
Retrocopy SSSSSYGSRR--SRSRSRG*GESYRVQRSRSKSRTR--RSRSRPRP--RSHSRSSERS----SRRRTRSE

Parental  AREKEKREKEKEKGKDKELFDIKRGESGSIKAGLEHLPPAEQAKARLQLVLEAAAKADEALKAKXRRKED
          ..................L.DIKRGESG.IKAGLEHLPPAEQA.ARLQLVL.AAA.ADEALKA..R..E.
Retrocopy SXXXXXXXXXXXXXXXXXLLDIKRGESGNIKAGLEHLPPAEQATARLQLVL*AAANADEALKAEERNEEE

Parental  QTTLVE--QVKRVKEIEAIESDSFVQQTFRSSKEVKKSVE-PRAVQPA
          .....E..Q............................S.E...AV.P.
Retrocopy AKRRKEEDQATLLEQVKRVKELEAIESDSFVQQTFRSSKEVKKAVEPS

Legend:

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

Expression

RNA-Seq

Echinops telfairi was not studied using RNA-Seq expression data.

ChIP-Seq

Echinops telfairi was not studied using ChIP-Seq data.

EST

Echinops telfairi was not studied using EST data.

TSS

Echinops telfairi was not studied using FANTOM5 data.

Lab

retro_etel_1555 was not experimentally validated.

Homology

Retrocopy orthology:

Echinops telfairi does not belong to any of the species groups (eutheria, teleost or neognath), studied for retrocopy-based homology. For more information about studied groups, please go to help section.

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Parental genes homology:

Parental genes homology involve 8 parental genes, and 22 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000004797	1 retrocopy	retro_cjac_553,
Cavia porcellus	ENSCPOG00000000876	2 retrocopies	retro_cpor_618, retro_cpor_671,
Echinops telfairi	ENSETEG00000017217	1 retrocopy	retro_etel_1555 ,
Homo sapiens	ENSG00000174891	1 retrocopy	retro_hsap_4281,
Mus musculus	ENSMUSG00000034544	1 retrocopy	retro_mmus_666,
Nomascus leucogenys	ENSNLEG00000004137	1 retrocopy	retro_nleu_2851,
Rattus norvegicus	ENSRNOG00000012639	2 retrocopies	retro_rnor_2454, retro_rnor_577,
Tupaia belangeri	ENSTBEG00000001973	13 retrocopies	retro_tbel_1285, retro_tbel_1372, retro_tbel_2078, retro_tbel_2400, retro_tbel_2545, retro_tbel_3145, retro_tbel_3313, retro_tbel_3748, retro_tbel_3834, retro_tbel_4317, retro_tbel_4458, retro_tbel_4494, retro_tbel_840,